Agents providing controls and standards for immuno-precipitation assays

ABSTRACT

Control agents for immuno-precipitation assays, methods of using the control agents and kits comprising the control agents are provided.

RELATED APPLICATIONS

This application is a continuation-in-part of international applicationnumber PCT/US2011/053950, filed Sep. 29, 2011, which claims the benefitunder 35 U.S.C. §119(e) of U.S. provisional application Ser. No.61/387,673, filed Sep. 29, 2010, each of which is incorporated byreference herein in its entirety.

GOVERNMENT SUPPORT

This invention was made with government support under U54 HG004570awarded by the National Institutes of Health and under U01 ES017155awarded by the National Institutes of Health. The government has certainrights in the invention.

BACKGROUND OF INVENTION

Chromatin immuno-precipitation (ChIP) is a powerful tool for evaluatinginteraction of proteins with specific genomic DNA regions in vivo, toprovide a better understanding of the mechanisms of gene regulation, DNAreplication, and DNA repair. The ChIP technique involves fixativetreatment of live cells with formaldehyde to chemically cross-linkDNA-bound proteins. The cells are then lysed, and the chromatin issheared mechanically or enzymatically, in order to reduce fragment sizeand increase resolution. The resultant sheared complexes are thenimmuno-precipitated with antibodies specific to the protein of interest,and the DNA fragments are analyzed, e.g. using real time PCR,sequencing, or microarray hybridization. The ChIP protocol wasintroduced in 1988 (Solomon M J et al. Cell. 1988 53(6):937-47). Itspower and widespread use has increased significantly with theincorporation of nucleic acid detection assays such as microarrays andsequencing that have enabled the method to be scaled genome-scale orgenome-wide.

SUMMARY OF INVENTION

Aspects of the invention relate to control agents forimmuno-precipitation (IP) assays. In certain embodiments, theimmuno-precipitation assay is a chromatin immuno-precipitation assay(ChIP). The control agents provided herein comprise a polypeptidesegment providing an antigen and a oligonucleotide segment comprising aunique sequence that allows identification of the control agent. The twosegments are linked together by a linker molecule. The antigen maycomprise exclusively unmodified amino acids or one or more modifiedamino acids. In certain embodiments, amino acid modifications are thosecommon during post-translational protein modification in vivo, such asacetylation, methylation (e.g. mono-, di-, tri-), phosphorylation,ubiquitination (e.g. mono-, di-, tri-, poly-), sumoylation,ADP-ribosylation, citullination, and cis-trans isomerization. In otherembodiments, antigens may comprise specific mutations of a wild-typeamino acid sequence, such as point mutations. In yet other embodiments,antigens may comprise exclusively wild-type amino acid sequence. Thepolypeptide segment comprising the antigen may comprise amino acidfragments derived from histone proteins or non-histone proteins. Incertain embodiments, the polypeptide segment comprising the antigenconsists of at least 5 amino acids. In certain embodiments, theoligonucleotide segment comprising the unique identifier consists of atleast 10 nucleotides. In certain embodiments, the oligonucleotidesegment further comprises one or more amplification sequences.

Further provided herein are methods of using the control agents in IPassays, methods of using the control agents in screening antibodies forsuitability in IP assays, and methods of using the control agents tonormalize data obtained from performing ChIP assays.

Further provided herein are kits comprising the control agents describedherein for use in IP assays.

In certain aspects the invention provides polypeptide-oligonucleotideconjugate of the formula:

A-L-N,

wherein A is a polypeptide comprising 5 amino acids, L is a linker, andN is an oligonucleotide comprising 10 nucleotides, wherein the sequenceof nucleotides of N uniquely identifies an amino acid sequence and/oramino acid modification of A. In certain embodiments, A is 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45,46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63,64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81,82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99,100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113,114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127,128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141,142, 143, 144, 145, 146, 147, 148, 149, or 150 amino acids. In certainembodiments, A is 5-15, 5-25, 5-50, 5-100, 5-250, 5-500, 5-1000, 5-2500,5-5000, 5-10,000, 5-25,000, or 5-50,000 amino acids.

In certain embodiments, A comprises a modified amino acid. In certainembodiments, the modification is a post-translational modification. Insuch embodiments, the modification may be selected from the groupconsisting of acetylation, methylation (mono-, di-, tri-),phosphorylation, ubiquitination (mono-, di-, tri-, poly-), sumoylation,ADP-ribosylation, citullination, biotinylation, and cis-transisomerization.

In certain embodiments, A comprises an amino acid sequence derived froma histone protein selected from the group consisting of histone H1, H2A,H2AX, H2B, H3, H4. In certain embodiments, the amino acid sequence isderived from the amino terminus, whereas in other embodiments, the aminoacid sequence is derived from the carboxyl terminus. In certainembodiments, A comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,34, 35, or 36 amino acids of any one sequence selected from the groupconsisting of SGRGKQGCKARAK (SEQ ID NO: 1), VLLPKKTESHHKAKGK (SEQ ID NO:2), PEPAKSAPAPKKGSKKAVTK (SEQ ID NO: 3), AVSEGTKAVTKYTSSK (SEQ ID NO:4), ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVK (SEQ ID NO: 5),QRLVREIAQDFKTDLRFQSSAVMALQEA (SEQ ID NO: 6),SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLA (SEQ ID NO: 7) and alterationsthereof, selected from: a conservative amino acid exchange, anon-conservative amino acid exchange, and/or an amino acid exchange of anatural amino acid to a non-natural amino acid. In certain embodiments,the altered amino acid sequence is 90%, 95%, 98%, or 99% identical toone of the amino acid sequences set forth in SEQ ID NOs: 1-7. In certainembodiments, the amino acid sequence is derived from a histone of amammal, a fish, a yeast, a plant, an insect, or a nematode.

In certain embodiments, A comprises:

X_(n)Y[M]X_(n),

wherein X is an amino acid, n is a number of amino acids, Y is amodified amino acid, M is a modification. In such embodiments, n is0-15, 0-25, 0-50, 0-100, 0-150, 0-250, 0-500, 0-1000, 0-2500, 0-5000,0-10,000, 0-25,000, or 0-50,000 amino acids. In such embodiments, M isselected from the group consisting of H1 (phospho S1+T3), H1 (phosphoS35), H1 (acetyl K63); H2A (asymmetric di methyl R3), H2A (symmetric dimethyl R3), H2A (acetyl K5), H2A (mono methyl R17), H2A (symmetric dimethyl R77), H2A (Hydroxy P26), H2A (mono methyl K125), H2A (tri methylK125), H2A (mono methyl K127), H2A (tri methyl K127), H2A (phosphoS129); H2B (acetyl K5), H2B (di methyl K5), H2B (Hydroxy P10), H2B (dimethyl K43); H3 (mono methyl R2), H3 (citrulline 2+8+17), H3 (monomethyl K4), H3 (di methyl K4), H3 (tri methyl K4), H3 (di+tri methylK4), H3 (acetyl K9), H3 (acetyl K9, phospho S10), H3 (mono methyl K9),H3 (di methyl K9), H3 (tri methyl K9), H3 (phospho S10), H3 (asymmetricdi methyl R17), H3 (acetyl K18), H3 (acetyl K27), H3 (di methyl K27), H3(tri methyl K27), H3 (mono methyl K27, tri methyl K27+K4), H3 (monomethyl K36), H3 (tri methyl K36), H3 (Hydroxy P38), H3 (mono methylK79), H3 (di methyl K79), H3 (tri methyl K79), H3 (mono+di+tri methylK79), H3 (Hydroxy P121), H3 (tri methyl K122); H4 (symmetric di methylR3), H4 (acetyl K8), H4 (acetyl K12), H4 (mono methyl K20), H4 (trimethyl K20), H4 (phospho T30), H4 (Hydroxy P32), H4 (tri methyl K59), H4(phospho T80), H4 (acetyl K91), and H4 (phospho T96).

In certain embodiments, N of the polypeptide-oligonucleotide conjugateof any one of the preceding embodiments is 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53,54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71,72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89,90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105,106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119,120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133,134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147,148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161,162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175,176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189,190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203,204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217,218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231,232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245,246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259,260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273,274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287,288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301,302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315,316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329,330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343,344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357,358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371,372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385,386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399,400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413,414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427,428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441,442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455,456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468, 469,470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480, 481, 482, 483,484, 485, 486, 487, 488, 489, 490, 491, 492, 493, 494, 495, 496, 497,498, 499, or 500 nucleotides. In certain embodiments, N is 10-25, 10-50,10-100, 10-250, 10-500, 10-1000, 10-2500, 10-5000, 10-10,000, 10-25,000,10-50,000 or 10-100,000 nucleotides.

In certain embodiments, N comprises a nucleotide sequence U thatuniquely identifies an amino acid sequence and/or amino acidmodification of A. In certain embodiments, the unique nucleotidesequence U consists of about 20, about 30, about 40, about 50, about 60,about 70, about 80, about 90, or about 100 nucleotides. In certainembodiments, the unique nucleotide sequence U is from 10 nucleotides to500 nucleotides, from 20 to 200, from 30 to 300, from 40 to 400, from 15to 150, from 50 to 100, from 25 to 75, or from 45 to 65 nucleotides. Incertain embodiments, U is 10-1000, 10-2500, 10-5000, 10-10,000,10-25,000, or 10-50,000 nucleotides.

In certain embodiments, N comprises:

x_(n)P1-U-P2x_(n),

wherein x is any nucleotide, n is a number of nucleotides, P1 and P2 areprimer sequences, and U is a unique sequence of nucleotides. In certainembodiments, the primer sequences P1 and P2 each are independently 15,16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,34, or 35 nucleotides. In certain embodiments, P1 and P2 each areindependently 10-35, 10-40, 10-45, 10-50, 10-55, 10-60, 10-65, 10-70,10-75, 10-100, 10-250, 10-500, or 10-1000 nucleotides. In certainembodiments, the primer sequences P1 and P2 each comprise 10nucleotides. In certain embodiments, U is 10-50, 10-100, 10-250, 10-500,10-1000, 10-2500, 10-5000, 10-10,000, 10-25,000, or 10-50,000nucleotides. In certain embodiments, n is 0-15, 0-25, 0-50, 0-100,0-150, 0-250, 0-500, 0-1000, 0-2500, 0-5000, 0-10,000, 0-25,000, or0-50,000 amino acids.

In certain embodiments, N comprises:

x_(n)Ux_(n),

wherein x is any nucleotide, n is a number of nucleotides and U is aunique sequence of nucleotides. In certain embodiments, U is 10-50,10-100, 10-250, 10-500, 10-1000, 10-2500, 10-5000, 10-10,000, 10-25,000,or 10-50,000 nucleotides. In certain embodiments, n is 0-15, 0-25, 0-50,0-100, 0-150, 0-250, 0-500, 0-1000, 0-2500, 0-5000, 0-10,000, 0-25,000,or 0-50,000 amino acids.

In certain embodiments, A which comprises either X_(n) or X_(n)Y[M]X_(n)is joined via a linker L with a N, comprising x_(n)P1-U-P2x_(n).

In certain embodiments, A-L-N is:

x_(na)Y[M]X_(na)-L-x_(nn)P1-U-P2x_(nn),

wherein X is an amino acid; na is a number of amino acids; Y is amodified amino acid; M is a modification, wherein X_(na)Y[M]X_(na) isleast 5 amino acids; L is a linker; x is any nucleotide, nn is a numberof nucleotides, P1 and P2 are primer sequences, and U is a uniquenucleotide sequence. In certain embodiments, U is 10-50, 10-100, 10-250,10-500, 10-1000, 10-2500, 10-5000, 10-10,000, 10-25,000, or 10-50,000nucleotides. In certain embodiments, P1 and P2 each are independently10-35, 10-40, 10-45, 10-50, 10-55, 10-60, 10-65, 10-70, 10-75, 10-100,10-250, 10-500, or 10-1000 nucleotides. In certain embodiments, na is0-15, 0-25, 0-50, 0-100, 0-150, 0-250, 0-500, 0-1000, 0-2500, 0-5000,0-10,000, 0-25,000, or 0-50,000 amino acids. In certain embodiments, nnis 0-15, 0-25, 0-50, 0-100, 0-150, 0-250, 0-500, 0-1000, 0-2500, 0-5000,0-10,000, 0-25,000, 0-50,000 or 0-100,000 nucleotides.

In certain embodiments, L is a chemical linker. In certain embodiments,the linker comprises two reactive terminal groups that can chemicallyinteract with the two segments A and N. In certain embodiments, thelinker L is 1-10 atoms, 1-25 atoms, 1-50 atoms, 1-100 atoms, 1-200atoms, 1-500 atoms, 1-1000 atoms, 1-5000 atoms, 1-10,000 atoms, 1-50,000atoms, or 1-100,000 atoms in length.

In certain aspects the invention provides sets ofpolypeptide-oligonucleotide conjugates described herein comprising atleast two of the polypeptide-oligonucleotide conjugates of any of thepreceding embodiments. In certain embodiments, the set comprises atleast 5, at least 10, at least 15, at least 20, at least 25, at least30, at least 35, at least 40, at least 50, at least 60, at least 70, atleast 80, at least 90, at least 100, at least 125, at least 150, atleast 175, or at least 200 of the polypeptide-oligonucleotide conjugatesof any of the preceding embodiments.

In certain aspects the invention provides kits comprising thepolypeptide-oligonucleotide conjugate described herein. In certainembodiments, the kits further contain one or more reagents necessary toperform a ChIP assay and/or one or more reagents necessary to performchromatin fragment modification. In certain embodiments, the one or morekit reagents necessary to perform the ChIP assay are RNase A, ProteinaseK, formaldehyde, glycine, PBS, cell lysis buffer, Triton X-100, proteaseinhibitor cocktails, wash buffer, elution buffer, or a ChIP antibody. Incertain embodiments, the one or more kit reagents necessary to performthe chromatin fragment modification are Klenow DNA polymerase, DNApolymerase, T4 ligase, T4 polynucleotide kinase, T4 DNA polymerase,Klenow fragment 3′ to 5′ exo minus, enzyme reaction buffer, dATP, dNTPs,ultrapure water, TE, PCR or sequencing specific adapter, or a PCR orsequencing primer. In certain embodiments, the kits of any of thepreceding embodiments, contain 1, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50,55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 200, 300, 400, 500, 1000different polypeptide-oligonucleotide conjugates of the formula A-L-Ndescribed herein.

In certain aspects the invention provides the use of apolypeptide-oligonucleotide conjugate described herein in animmuno-precipitation assay.

In certain aspects the invention provides a method of validating achromatin immuno-precipitation (ChIP) assay result, wherein the methodincludes:

(a) obtaining an input sample of the genomic material of interest and ofone or more of the polypeptide-oligonucleotide conjugates describedherein,(b) performing a ChIP assay, thereby processing, in parallel to thegenomic material of interest of (a), the one or morepolypeptide-oligonucleotide conjugates of (a),(c) obtaining a processed sample of the polypeptide-oligonucleotideconjugate and the genomic material of interest processed in (b), and(d) analyzing the samples obtained in (c), thereby obtaining a valueand/or signal for each of the analyzed processed samples, and(e) validating the ChIP assay result based on the value and/or signalobtained in (d).

In certain embodiments, the method includes a validation step thatincludes one or more comparisons of the value and/or signal of the inputsample and the value and/or signal of the processed sample of C1 withthe value and/or signal of the input sample and the value and/or signalof the processed sample of C2, wherein

(a) C1 is the genomic material of interest (e.g. immuno-precipitatednucleic acid, such as DNA) and C2 is a polypeptide-oligonucleotideconjugate, wherein C2 is a polypeptide-oligonucleotide conjugateimmunoprecipitated with an antibody that is specific for thepolypeptide-oligonucleotide conjugate (C2S), or C2 is apolypeptide-oligonucleotide conjugate immunoprecipitated with anantibody that is non-specific for the polypeptide-oligonucleotideconjugate (C2N), and/or(b) C1 is a polypeptide-oligonucleotide conjugate immunoprecipitatedwith an antibody that is specific for the polypeptide-oligonucleotideconjugate and C2 is a polypeptide-oligonucleotide conjugateimmunoprecipitated with an antibody that is non-specific for thepolypeptide-oligonucleotide conjugate.

In certain embodiments, the methods described herein allow to concludethat when

(i) the value and/or signal of the processed sample in (a) of C1 and C2Sis significantly higher than the value and/or signal of the input sample(e.g. non-iimunoprecipitated nucleic acid or cell extract, such as wholecell extract), then the genomic sample comprises an epitope specific forthe antibody that is specific for C2S,(ii) the value and/or signal of the processed sample in (a) of C1 andC2N is significantly higher than the value and/or signal of the inputsample, then the genomic sample is non-specifically amplified orimmunoprecipitated and the value or signal obtained is discarded,(iii) the value and/or signal of the processed sample in (a) of C1 isnot significantly higher than the value and/or signal of the inputsample and the value and/or signal of the processed sample of C2S issignificantly higher than the value and/or signal of the input sample,then the genomic sample does not comprise an epitope specific for theantibody that is specific for C2S,(iv) the value and/or signal of the processed sample in (a) of C1 issignificantly higher than the value and/or signal of the input sampleand the value and/or signal of the processed sample of C2S is notsignificantly higher than the value and/or signal of the input sample,then the genomic sample is non-specifically amplified orimmunoprecipitated and the value or signal obtained is discarded,(v) the value and/or signal of the processed sample in (b) of C1 issignificantly higher than the value and/or signal of the input sampleand the value and/or signal of the processed sample of C2 is notsignificantly higher than the value and/or signal of the input sample,then the data obtained is analyzed,(vi) the value and/or signal of the processed sample in (b) of C1 and C2is significantly higher than the value and/or signal of the inputsample, then the data obtained is not analyzed and is discarded.

In certain embodiments, the value and/or signal for the input sample andthe processed sample are calculated as ratios.

In certain aspects the invention provides a method of screening anantibody for use in a chromatin immuno-precipitation (ChIP) assay, themethod includes:

(a) contacting an antibody specific for an antigen of interest with oneor more polypeptide-oligonucleotide conjugate of any one of claims 1 to29, wherein at least one of the polypeptide-oligonucleotide conjugatescomprises the antigen of interest and at least onepolypeptide-oligonucleotide conjugate does not comprise the antigen ofinterest(b) performing a ChIP assay, thereby processing the oligonucleotideconjugate comprising the antigen of interest and thepolypeptide-oligonucleotide conjugate not comprising the antigen ofinterest in parallel,(c) obtaining a processed sample of the polypeptide-oligonucleotideconjugate in (b),(d) analyzing the samples obtained in (c), thereby obtaining a valueand/or signal for each the oligonucleotide conjugate comprising theantigen of interest and the polypeptide-oligonucleotide conjugate notcomprising the antigen of interest, and(e) comparing the obtained values and/or signals,wherein when the value and/or signal obtained form the oligonucleotideconjugate comprising the antigen of interest is significantly higherthan the value and/or signal obtained form the oligonucleotide conjugatenot comprising the antigen of interest, then the antibody is useful in aChIP assay. In certain embodiments, performing a ChIP assay in (b)comprises one or more steps of:(a) immobilizing the antibody and specifically bound material,(b) reducing the amount of non-specifically bound material,(c) releasing the specifically bound material from the antibody,(d) fragmenting proteinaceous material, and/or(e) purifying nucleic acid material.

In certain aspects the invention provides a method of normalizingchromatin immuno-precipitation (ChIP) assay data, wherein the methodincludes:

(a) obtaining an input sample of the genomic material of interest and ofone or more of the polypeptide-oligonucleotide conjugates of any one ofclaims 1 to 29,(b) performing a ChIP assay, thereby processing, in parallel to thegenomic material of interest in (a), the one or morepolypeptide-oligonucleotide conjugates of (a),(c) obtaining a processed sample of the polypeptide-oligonucleotideconjugate and the genomic material of interest processed in (b),(d) analyzing the samples obtained in (c), thereby obtaining a valueand/or signal for each of the analyzed processed samples, and(e) normalizing the values and/or signals obtained in (d) for each ofthe processed samples using the values obtained in (d) for each of theinput samples. In certain embodiments, parallel processing in (b)includes contacting the genomic material with the one or morepolypeptide-oligonucleotide conjugates. In certain embodiments, thecontacting of the genomic material with the one or morepolypeptide-oligonucleotide conjugates is performed after fragmentationof the genomic material and before the resulting sample is contactedwith an antibody.

In certain embodiments, performing a ChIP assay in (b) comprises one ormore steps of:

(a) fragmenting genomic material of interest,(b) contacting the fragmented genomic material and the one or morepolypeptide-oligonucleotide conjugates with an antibody,(c) immobilizing the antibody and specifically bound material,(d) reducing the amount of non-specifically bound material,(e) releasing the specifically bound material from the antibody,(f) reversing a previous cross-linking reaction,(g) fragmenting proteinaceous material, and/or(h) purifying nucleic acid material.

In certain embodiments, analyzing the processed sample in (d) comprisesperforming a polymerase-chain reaction, a sequencing reaction, and/or ahybridization reaction. In certain embodiments, normalizing in (e)comprises calculating ratios for input sample and processed sample forthe genomic material and the one or more polypeptide-oligonucleotideconjugates.

Other aspects of the invention relate to control agents forimmuno-precipitation (IP) assays, including but not limited to RNA-IPfollowed by sequencing (RIP-seq), methylated-DNA IP followed bysequencing (mDIP-seq), bisulphite sequencing (BS-seq), High-throughputsequencing of RNA isolated by crosslinking IP (HITS-CLIP),formaldehyde-assisted isolation of regulatory elements followed bysequencing (FAIRE-seq), and micrococcal nuclease digestion followed bysequencing (MNase-seq). Control agents provided herein comprise theformula:

X-B or B-X,

where X is a molecule (e.g., polypeptide, such as A described above, ora polynucleotide), and B (also referred to as “barcode”) is anoligonucleotide (e.g., DNA or RNA) comprising, for example, 10nucleotides, wherein the sequence of nucleotides of B uniquelyidentifies X. In some configurations, a linker L is used to conjugate Band X. Examples of control agents include, but are not limited to,barcoded DNA-peptide conjugates, barcoded RNA-peptide conjugates,barcoded methylated DNA oligos, and assembled nucleosomes conjugated tobarcoded DNA.

Additional aspects and embodiments of the invention are described ininternational application number PCT/US2011/054072, filed Sep. 29, 2011,which claims the benefit under 35 U.S.C. §119(e) of U.S. provisionalapplication Ser. No. 61/387,689, filed Sep. 29, 2010, each of which isincorporated by reference herein in its entirety.

This application refers to various issued patents, published patentapplications, journal articles, and other publications, all of which areincorporated herein by reference for the purposes cited herein.

BRIEF DESCRIPTION OF THE FIGURES

The patent or application file contains at least one drawing executed incolor. Copies of this patent or patent application publication withcolor drawings will be provided by the Office upon request and paymentof the necessary fee.

FIG. 1 is a schematic depicting some common posttranslationalmodifications of human nucleosomal histones. The modifications includeacetylation (ac), methylation (me), phosphorylation (ph) andubiquitination (ub1). Globular domains of each core histone arerepresented as ovals.

FIG. 2 is a schematic depicting some common posttranslationalmodifications of histones and the names of the enzymes thought to beresponsible for the modification. Globular domains of each core histoneare represented as ovals.

FIG. 3A is a schematic depicting various modifications that may occur atspecific amino acid residues. FIG. 3B is a schematic depicting themodifications listed in FIG. 3A at their location on the histones.

FIG. 4 is a schematic depicting various kits. The circles represent oneor more receptacles for one or more reagents. The dotted lines representvarious expanded kits that further contain optional receptacles/reagentsthat may be combined in any number or order with thepolypeptide-oligonucleotide conjugate A-L-N.

DEFINITIONS

“Amino acids” may be referred to herein by either their commonly knownthree letter symbols or by the one-letter symbols recommended by theIUPAC-IUB Biochemical Nomenclature Commission. Amino acid residues inproteins or peptides are abbreviated as follows: phenylalanine is Phe orF; leucine is Leu or L; isoleucine is Ile or I; methionine is Met or M;valine is Val or V; serine is Ser or S; proline is Pro or P; threonineis Thr or T; alanine is Ala or A; tyrosine is Tyr or Y; histidine is Hisor H; glutamine is Gln or Q; asparagine is Asn or N; lysine is Lys or K;aspartic acid is Asp or D; glutamic Acid is Glu or E; cysteine is Cys orC; tryptophan is Trp or W; arginine is Arg or R; and glycine is Gly orG. For further description of amino acids, see Proteins: Structure andMolecular Properties by Creighton T. E. (1983), W. H. Freeman & Co., NewYork, incorporated herein by reference.

The term “amino acid” refers to naturally occurring and non-naturalamino acids, as well as amino acid analogs and amino acid mimetics thatfunction in a manner similar to the naturally occurring amino acids.Naturally encoded amino acids are the 20 common amino acids (alanine,arginine, asparagine, aspartic acid, cysteine, glutamine, glutamic acid,glycine, histidine, isoleucine, leucine, lysine, methionine,phenylalanine, proline, serine, threonine, tryptophan, tyrosine, andvaline) and pyrrolysine and selenocysteine. Amino acid analogs refers tocompounds that have the same basic chemical structure as a naturallyoccurring amino acid, i.e., an a carbon that is bound to a hydrogen, acarboxyl group, an amino group, and an R group, such as, homoserine,norleucine, methionine sulfoxide, methionine methyl sulfonium. Suchanalogs have modified R groups (such as, norleucine) or modified peptidebackbones, but retain the same basic chemical structure as a naturallyoccurring amino acid.

A “non-natural amino acid” refers to an amino acid that is not one ofthe 20 common amino acids, pyrrolysine or selenocysteine; The term“non-natural amino acid” includes, but is not limited to, amino acidsthat occur naturally by modification of a naturally encoded amino acid(including but not limited to, the 20 common amino acids or pyrrolysineand selenocysteine) but are not themselves incorporated into a growingpolypeptide chain by the translation complex. Examples ofnaturally-occurring amino acids that are not naturally-encoded include,but are not limited to, N-acetylglucosaminyl-L-serine,N-acetylglucosaminyl-L-threonine, and O-phosphotyrosine.

As to amino acid sequences, one of skill will recognize that individualsubstitutions, deletions or additions to a nucleic acid, peptide,polypeptide, or protein sequence which alters, adds or deletes a singleamino acid or a small percentage of amino acids in the encoded sequenceis a “conservatively modified variant” where the alteration results inthe substitution of an amino acid with a chemically similar amino acid.Conservative substitution tables providing functionally similar aminoacids are known to those of ordinary skill in the art. Suchconservatively modified variants are in addition to and do not excludepolymorphic variants, interspecies homologs/orthologs, and alleles ofthe agents described herein.

Conservative amino acid substitutions are amino acid substitution inwhich the substituted amino acid residue is of similar charge as thereplaced residue and/or is of similar or smaller size than the replacedresidue. Conservative substitutions of amino acids include substitutionsmade amongst amino acids within the following groups: (a) the smallnon-polar amino acids, A, M, I, L, and V; (b) the small polar aminoacids, G, S, T, and C; (c) the amido amino acids, Q and N; (d) thearomatic amino acids, F, Y, and W; (e) the basic amino acids, K, R, andH; and (f) the acidic amino acids, E and D. Substitutions which arecharge neutral and which replace a residue with a smaller residue mayalso be considered conservative substitutions even if the residues arein different groups (e.g., replacement of phenylalanine with the smallerisoleucine). Methods for making amino acid substitutions, additions, ordeletions are well known in the art, e.g., polymerase chain reaction(PCR)-directed methods (Molecular Biology: Current Innovations andFuture Trends. by Griffin A. M. and Griffin H. G. (1995) HorizonScientific Press, Norfolk, U.K; Modern Genetic Analysis. by Griffith A.J., Second Edition, (2002) H. Freeman and Company, New York, N.Y.).

An “antigen” as used herein may be any amino acid fragment (modified orunmodified) of 5 amino acids or more which are recognized by an antibodyor for which recognizing antibodies can be raised. In certainembodiments, antigens may comprise modifications of an amino acid, suchas acetylation, methylation (e.g. mono-, di-, tri-), phosphorylation,ubiquitination e.g. mono-, di-, tri-, poly-), sumoylation,ADP-ribosylation, citullination, biotinylation, and cis-transisomerization. In other embodiments, antigens may comprise specificmutations, such as point mutations. In other yet embodiments, antigensmay comprise wild-type amino acid sequence.

A “bifunctional linker” refers to a polymer comprising two discretefunctional groups that are capable of reacting specifically with othermoieties (including but not limited to, NH₂—, SH—, —COOH, —CO, and—C_(n)H_(n) groups) to form covalent or non-covalent linkages. Manyprocedures and linker molecules for attachment of various compounds topeptides are known. e.g. U.S. Pat. Nos. 4,671,958; 4,659,839; 4,680,338;and 4,569,789. A bi-functional linker or multi-functional linker may beany desired length or molecular weight, and may be selected to provide aparticular desired spacing or conformation between one or more moleculeslinked to the polypeptide.

The terms “polypeptide,” “peptide” and “protein” are usedinterchangeably herein to refer to a polymer of amino acid residues.That is, a description directed to a polypeptide applies equally to adescription of a peptide and a description of a protein, and vice versa.The terms apply to naturally occurring amino acid polymers as well asamino acid polymers in which one or more amino acid residues is anon-natural amino acid. As used herein, the terms encompass amino acidchains of any length, including full length proteins, wherein the aminoacid residues are linked by covalent peptide and/or pseudopeptide bonds.

The term “post-translational modification” refers to any modification ofa natural or non-natural amino acid that occurs or would occur to suchan amino acid after it has been incorporated into a polypeptide chain invivo or in vitro. Such modifications include, but are not limited to,acetylation, methylation (e.g. mono-, di-, tri-), phosphorylation,ubiquitination (e.g. mono-, di-, tri-, poly-), sumoylation,ADP-ribosylation, citullination, biotinylation, and cis-transisomerization. Such modifications may be introduced synthetically, e.g.chemically, during polypeptide synthesis or enzymatically afterpolypeptide synthesis or polypeptide purification.

By “screen” or “screening” is meant to test a compound (e.g. anantibody) with a particular characteristic or desired property. Testingmay be conducted in vivo or in vitro, for example in a biochemicalassay, such as those described herein. These characteristics or desiredproperties of the compound (e.g. antibody) may be chemical, biological,or physical in nature or a combination thereof. Desired characteristicsor desired properties of antibodies in ChIP may, for example, be highaffinity and/or high specificity for a particular antigen of interest.

DETAILED DESCRIPTION OF CERTAIN EMBODIMENTS OF THE INVENTION

Controls for immuno-precipitation assays, e.g., ChIP assays, that arecurrently used have several major drawbacks with regard to theirspecificity and their ability to distinguish between true and falsenegative or positive results obtained by the procedure. For example, apositive antibody control for the ChIP technique that is commonly usedis Histone H3 (tri methyl K4) when analyzing active genes. As a negativecontrol, use of an antibody that recognizes a non-chromatin epitope,such as an anti-GFP antibody, is common. Such control antibodieshowever, do not validate the ChIP procedure (i.e. are not positive andnegative controls for the success of the ChIP experiment) per se. Forexample, if Histone H3 tri methyl K4 is absent at the particular genomiclocus of interest, then even a highly efficient and specific ChIPantibody will not immuno-precipitate chromatin from this region and thuswill not be an appropriate positive control. An anti-GFP antibody willnot provide a good negative control for non-specific binding ofantibodies directed to histone modifications. Further, chromatinremodeling may move or remove histones at a particular locus e.g. anactive promoter, so use of a control antibody against a non-modifiedhistone, such as Histone H3, may be necessary to confirm thepreservation of nucleosomes at particular genomic loci. If a ChIP signalis weak or non-existent, troubleshooting may include use of differentantibody, optimizing of the cross-linkage time course, thefragmentation, binding, wash, and/or elution conditions. Current ChIPprotocols recommend using purified histone H3 and H1 as positivecontrols for the quality of the experimental histone preparation, whenanalyzing histone modifications.

Existing technologies for ChIP antibody validation and ChIP qualitycontrols, e.g. using primer and probe sets specific for particular genesor chromatin regions. For example, probes and primers may be providedfor certain housekeeping gene loci, tissue-specific gene loci,heterochromatic loci or gamma actin loci (Abcam, Cambridge Mass.). Thesecontrol kits can be limiting in that the source material can only bedetected by the primer/probe pairs in a species-specific manner (e.g. tohuman genes, such as hsGAPDH, hsMyoD, hsSATa, and hsAct1) and in thatthe histone modification, for which a control is necessary, needs to bedetermined prior to conducting the ChIP assay. For example, hsGAPDHprimer/probe sets may provide a positive control for a specific histonemodification associated with active gene transcription, such as HistoneH3 K9 acetylation, and may provide a negative control for a specifichistone modification associated with silencing, such as Histone H3 K9tri methylation. hsMyoD primer/probe sets may provide a positive controlfor a specific histone modification associated with gene silencing, suchas Histone H3 K27 dimethylation, and may provide a negative control fora specific histone modification associated with active genetranscription, such as Histone H3 K9 acetylation. hsSATa primer/probesets may provide a positive control for a specific histone modificationassociated with heterochromatin, such as Histone H3 K9 tri methylation,and may provide a negative control for a specific histone modificationsassociated with active gene transcription, such as Histone H3 K4 trimethylation.

These controls are based on empirically acquired knowledge of specificgene regions and since biological systems are dynamic, these controlscan vary, for example, between cell types or between the same cellsexposed to different conditions. These controls are not available forall of the known histone modifications. Moreover, it is very difficultto obtain and/or use such controls for assays that analyze non-histoneproteins, such as DNA-binding proteins (chromatin-associated factors,e.g. transcription factors, activator/repressor complex constituents,DNA replication or DNA repair factors, etc.) and non-histonemodifications, such as, for example, post-translational modifications oftranscription factors.

Further, as it is difficult to combine these controls in cases involvingseveral modifications that are probed in a ChIP assay these controlexperiments would need to be conducted sequentially, requiring moresample and more hands-on time.

Polypeptide-Oligonucleotide Conjugates as Controls for IP Assays—e.g.,ChIP:

It would be a distinct advantage to be able to monitor the steps of anChIP protocol and its efficiency using just one set of antibodies, forexample those that are directed to the histone modification of interest,and to have specific control agents that can undergo all the processsteps required for ChIP in parallel to the genomic material.Pre-determined amounts of such control could, for example, be added tothe assay at the beginning of the immuno-precipitation procedure (e.g.at the step when fragmented chromatin is contacted with the ChIPantibody). Further it would be useful to provide a pool of controls forseveral histone modifications that can be processed in parallel withoutthe need to determine the control prior to performing the ChIP assay.

Provided herein are IP assays (e.g., ChIP assays) control agents thatare i) specific for an antigen of interest (e.g. a post-translationalhistone modification or non-histone protein modification andcorresponding unmodified sequences) and ii) can be pooled. In certainembodiments, the ChIP assays control agents may be provided as part of akit, for example a kit that comprises one or more additional reagentsnecessary to perform ChIP assays and or nucleic acid sequence analysis.

Provided herein are polypeptide-oligonucleotide conjugates of thegeneral formula:

A-L-N,

wherein “A” is a polypeptide of at least 5 amino acids, “L” is a linker,and “N” is an oligonucleotide of at least 10 bases as ChIP assayscontrol agents.

“A” as used herein consists of at least 5 amino acids. In certainembodiments, A is 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37,38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55,56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73,74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91,92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107,108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121,122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135,136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, or150 amino acids. In certain embodiments, A is 151 or more amino acids.In certain embodiments, A is 5-15, 5-25, 5-50, 5-100, 5-250, 5-500,5-1000, 5-2500, 5-5000, 5-10,000, 5-25,000, 5-50,000 or 5-100,000 aminoacids.

In certain embodiments, A comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,12, 13, 14, 15, 16, 18, 19, 20 or more amino acids at least in partderived from a histone protein, such as, for example, histone H2A, H2B,H3, or H4. In certain embodiments, A comprises 5-15, 5-25, 5-50, 5-100,5-250, 5-500, 5-1000, 5-2500, 5-5000, 5-10,000, 5-25,000, or 5-50,000amino acids at least in part derived from a histone protein, such ashistone H2A, H2B, H3, or H4. In certain embodiments, A comprises 1, 2,3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20 or more (upto the total amino acid sequence of the histone) amino acids derivedfrom the N-terminus of a histone protein, such as the N-terminus ofhistone H2A, H2B, H3, or H4. In other embodiments, A comprises 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20 or more (up tothe total amino acid sequence of the histone) amino acids derived fromthe C-terminus of a histone protein, such as the C-terminus of histoneH2A, H2B, H3, or H4. In certain embodiments, A comprises an amino acidsequence of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18,19, 20 or more (up to 36) amino acids of the following sequences:

H2A N-terminus: (SEQ ID NO: 1) SGRGKQGCKARAK H2A C-terminus:(SEQ ID NO: 2) VLLPKKTESHHKAKGK H2B N-terminus: (SEQ ID NO: 3)PEPAKSAPAPKKGSKKAVTK H2B C-terminus: (SEQ ID NO: 4) AVSEGTKAVTKYTSSKH3 N-terminus: (SEQ ID NO: 5) ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKH3 globular domain: (SEQ ID NO: 6) QRLVREIAQDFKTDLRFQSSAVMALQEAH4 N-terminus: (SEQ ID NO: 7) SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLA

In certain embodiments, A comprises an amino acid sequence of 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20 or more (up to36) amino acids of SEQ ID NOs: 1-7, wherein one or more of the aminoacids is modified. In certain embodiments, the one or more modificationis an acetylation, a methylation (e.g. mono-, di-, tri-), aphosphorylation, or an ubiquitination (e.g. mono-, di-, tri-, poly-),sumoylation, ADP-ribosylation, citullination, biotinylation, orcis-trans isomerization.

In certain embodiments, A comprises:

X_(n)Y[M]X_(n),

wherein X is an amino acid, n is a number of amino acids, Y is amodified amino acid, M is a modification. “n” in certain embodiments, is0-15, 0-25, 0-50, 0-100, 0-150, 0-250, 0-500, 0-1000, 0-2500, 0-5000,0-10,000, 0-25,000, or 0-50,000 amino acids.

Non-limiting examples of A comprising either no modifications or one ormore modifications are:

1) Non-Limiting Examples for a Derived from H2a are:

(SEQ ID NO: 8) X_(n)S[ph]GRGX_(n,) (SEQ ID NO: 9) X_(n)GRGK[ac]QGCX_(n,)(SEQ ID NO: 10) X_(n)S[ph]GRGKQGCX_(n,) (SEQ ID NO: 11)X_(n)SGRGK[ac]QGCX_(n,) (SEQ ID NO: 12) X_(n)QGCK[ac]ARAX_(n,)(SEQ ID NO: 13) X_(n)K[ub]TESX_(n,) (SEQ ID NO: 14) X_(n)KT[ph]ESHX_(n,)(SEQ ID NO: 15) X_(n)K[ub]TESHX_(n,) (SEQ ID NO: 16)X_(n)KT[ph]ESHX_(n,) (SEQ ID NO: 17) X_(n)SGRGKQGCKARAKX_(n)(SEQ ID NO: 18) X_(n)VLLPKKTESHHKAKGKX_(n)2) Non-Limiting Examples for a Derived from H2B are:

(SEQ ID NO: 19) X_(n)PEPAK[ac]SX_(n,) (SEQ ID NO: 20)X_(n)K[ac]GSKKX_(n,) (SEQ ID NO: 21) X_(n)KGS[ph]KKX_(n,)(SEQ ID NO: 22) X_(n)KGSK[ac]KX_(n,) (SEQ ID NO: 23)X_(n)K[ub]AVTKYTSSX_(n,) (SEQ ID NO: 24) X_(n)PAPKK[ac]GSKKAX_(n)(SEQ ID NO: 25) X_(n)PAPKKGSK[ac]KAVTKX_(n,,) (SEQ ID NO: 26)X_(n)KGS[ph]KKX_(n,) (SEQ ID NO: 27) X_(n)PEPAKSAPAPKKGSKKAVTKX_(n)(SEQ ID NO: 28) X_(n)AVSEGTKAVTKYTSSKX_(n)3) Non-Limiting Examples for a Derived from H3 are:

(SEQ ID NO: 29) X_(n)ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKX_(n),(SEQ ID NO: 30) X_(n)AR[me]TKX_(n), (SEQ ID NO: 31) X_(n)RT[ph]KX_(n),(SEQ ID NO: 32) X_(n)ARTK[me]QTAX_(n), (SEQ ID NO: 34)X_(n)ARKS[ph]TGGK[ac]APRX_(n) (SEQ ID NO: 35)X_(n)ARTKQTAR[me]KSTGGKAX_(n), (SEQ ID NO: 36)X_(n)RKST[ph]GGK[ac]AP_(n), (SEQ ID NO: 37)X_(n)ARTKQTARKSTGGKAPRKQLATKAAR[me]KSAPATGGVKX_(n), (SEQ ID NO: 38)X_(n)R[me]KSAX_(n), (SEQ ID NO: 39) X_(n)ARK[me]SAPX_(n),(SEQ ID NO: 40) X_(n)RK[ac]SAX_(n), (SEQ ID NO: 41) X_(n)S[ph]APAX_(n),(SEQ ID NO: 42) X_(n)QRLVREIAQDFKTDLRFQSSAVMALQEAX_(n) (SEQ ID NO: 43)X_(n)DFK[me]TDX_(n) (SEQ ID NO: 44) X_(n)K[me]TDLRFQSSX_(n)(SEQ ID NO: 45) X_(n)ARTKQTARKS[ph]TGGKAPRKQLATKAARKS[ph]APATGGVKX_(n)(SEQ ID NO: 46) X_(n)ARKS[ph]TGGK[ac]APRX_(n) (SEQ ID NO: 47)X_(n)RTK[me]QTARK[me]STX_(n) (SEQ ID NO: 48)X_(n)TK[me]QTARK[me]STGGKAPRKQLATKAARK[me]SAPATX_(n)4) Non-Limiting Examples for a Derived from H4 are:

(SEQ ID NO: 49) X_(n)S[ph]GRX_(n) (SEQ ID NO: 50)X_(n)SGR[me]GKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLAX_(n) (SEQ ID NO: 51)X_(n)SGRGK[ac]GGKX_(n) (SEQ ID NO: 52)X_(n)SGRGKGGK[ac]GLGKGGAKRHRKVLRX_(n) (SEQ ID NO: 53)X_(n)GKGGKGLGK[ac]GGAKRX_(n) (SEQ ID NO: 54)X_(n)GKGGAK[ac]RHRKVLRDNIQGITKX_(n) (SEQ ID NO: 55) X_(n)K[me]VLX_(n)(SEQ ID NO: 56) X_(n)KGLGKGGAKRHRK[me]VLRDNIQGITKX_(n) (SEQ ID NO: 57)X_(n)SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLAX_(n) (SEQ ID NO: 58)X_(n)GRGK[ac]GGKGLGK[ac]GGAKRHX_(n) (SEQ ID NO: 59)X_(n)GGK[ac]GLGKGGAK[ac]RHX_(n),

wherein [ac] is acetylation, [ph] is phosphorylation, [ub] isubiquitination, [me] is mono-, di- or tri-methylation, “X” is any aminoacid and “n” is a number of amino acids. “n” in certain embodiments, is0-15, 0-25, 0-50, 0-100, 0-150, 0-250, 0-500, 0-1000, 0-2500, 0-5000,0-10,000, 0-25,000, or 0-50,000 amino acids. Other modifications areknown in the art and are depicted for example in FIGS. 1, 2, and 3. Theexamples given here are for illustrative purposes only and are not meantto be limiting in any way. One of ordinary skill would know how tomodify the examples given here for A, for example, the number of aminoacids derived from the wild-type sequence of histones H2A, H2B, H3, andH4 exemplified here may be reduced or additional wild-type sequence maybe added (N- and/or C-terminal of the exemplified sequence), one or moreamino acids may be changed, e.g. using a conservative amino acidexchange or a non-conservative amino acid exchange (for examplespecies-specific exchanges to generate homologs/orthologs), one or morenon-natural amino acids may replace the amino acids exemplified,pseudopeptide units may be inserted, additional combinations ofmodifications e.g. acetylation, phosphorylation, ubiquitination, mono-,di- or tri-methylation, sumoylation, ADP-ribosylation, citullination,biotinylation, and cis-trans isomerization may be generated. Suchmodifications are well within the skills of an ordinary artisan (anddepicted in FIG. 3), any desired A segments may be generated and allsuch A segments are contemplated herein. For example, lysine (K) may beacetylated, sumoylated, ubiquitinated, biotinylated, or methylated;arginine (R) may be methylated, citullinated or ADP-ribosylated;glutamic acid (E) may be ADP-ribosylated; serine (S) and threonine (T)may be phosphorylated, and proline may be cis-trans-isomerated asdepicted in FIG. 3. Such modifications may be specific to certainhistones or all histones. Modifications may also be specific to certainspecies, such as mammals (human, mouse, rat, hamster, dog, cat, monkey,horse, sheep, cow), fish (e.g. zebrafish), yeast (e.g. Saccharomycescerevisiae, Schizosaccharomyces pombe, Candida albicans), plant (e.g.Arabidopsis thaliana, Nicotiana tabacum, corn, algae), fruit fly (e.g.Drosophila melanogaster), nematodes (Caenorhabditis elegans) and others.Further, additional A segments may be generated that comprise wild-typesequence of other histones, such as Histone H1 and H2AX. Histone H1, forexample comprises a modification at lysine 26 (K26[me]) and histone H2AXcomprises a modification at serine 139 (S139[ph]).

A segments for any known histone modification may be generated,including, but not limited to:

1) Modifications for Histone H1, for example H1 (phospho S1+T3), H1(phospho S35), H1 (acetyl K63);

2) Modifications for Histone H2A, for example H2A (asymmetric di methylR3), H2A (symmetric di methyl R3), H2A (acetyl K5), H2A (mono methylR17), H2A (symmetric di methyl R77), H2A (Hydroxy P26), H2A (mono methylK125), H2A (tri methyl K125), H2A (mono methyl K127), H2A (tri methylK127), H2A (phospho S129);

3) Modifications for Histone H2B, for example H2B (acetyl K5), H2B (dimethyl K5), H2B (Hydroxy P10), H2B (di methyl K43);

4) Modifications for Histone H3, for example H3 (mono methyl R2), H3(citrulline 2+8+17), H3 (mono methyl K4), H3 (di methyl K4), H3 (trimethyl K4), H3 (di+tri methyl K4), H3 (acetyl K9), H3 (acetyl K9,phospho S10), H3 (mono methyl K9), H3 (di methyl K9), H3 (tri methylK9), H3 (phospho S10), H3 (asymmetric di methyl R17), H3 (acetyl K18),H3 (acetyl K27), H3 (di methyl K27), H3 (tri methyl K27), H3 (monomethyl K27, tri methyl K27+K4), H3 (mono methyl K36), H3 (tri methylK36), H3 (Hydroxy P38), H3 (mono methyl K79), H3 (di methyl K79), H3(tri methyl K79), H3 (mono+di+tri methyl K79), H3 (Hydroxy P121), H3(tri methyl K122);

5) Modifications for Histone H4, for example H4 (symmetric di methylR3), H4 (acetyl K8), H4 (acetyl K12), H4 (mono methyl K20), H4 (trimethyl K20), H4 (phospho T30), H4 (Hydroxy P32), H4 (tri methyl K59), H4(phospho T80), H4 (acetyl K91), H4 (phospho T96).

“N” as used herein consists of at least 10 nucleotides. In certainembodiments, N is 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41,42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59,60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77,78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95,96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110,111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124,125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138,139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152,153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166,167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180,181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194,195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208,209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222,223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236,237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250,251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264,265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278,279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292,293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306,307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320,321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334,335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348,349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362,363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376,377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390,391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404,405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418,419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432,433, 434, 435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446,447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460,461, 462, 463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474,475, 476, 477, 478, 479, 480, 481, 482, 483, 484, 485, 486, 487, 488,489, 490, 491, 492, 493, 494, 495, 496, 497, 498, 499, or 500nucleotides. In certain embodiments, N is 10-25, 10-50, 10-100, 10-250,10-500, 10-1000, 10-2500, 10-5000, 10-10,000, 10-25,000, 10-50,000 or10-100,000 nucleotides.

In certain embodiments, N comprises a nucleotide sequence that is uniquefor a certain species (e.g. mammal, fish, yeast, plant, etc.) and/orproduces a product that when amplified (e.g. by PCR) is unique to thespecies. In certain embodiments, the unique nucleotide sequence of N maynot hybridize to a genomic fragment derived from the species. In certainembodiments, primers amplifying a unique portion of N will not amplify afragment of genomic DNA derived from the species. In certainembodiments, primers amplifying a unique portion of N will notefficiently amplify a fragment of genomic DNA derived from the species,such as, that the size of the amplified genomic fragment may be muchlarger than the size of the portion amplified in N.

In certain embodiments, the nucleotide sequence of N is unique to theamino acid sequence and/or amino acid modification of A, such that eachdifferent nucleotide sequence (N) in a set of nucleotide sequences (N1,N2, N3, N4, N5, . . . ) uniquely identifies a different amino acidsequence and/or amino acid modification (A) in a set of such amino acidsequences and/or amino acid modifications (A1, A2, A3, A4, A5, . . . ).For example, if A1 is X_(n)Y[M₁]X_(n), wherein X is an amino acid, n isa number of amino acids, Y is a modified amino acid, M₁ is amodification, and A2 is X_(n)Y[M₂]X_(n), wherein M₂ is a differentmodification form M₁, then N1 comprises a nucleotide sequence that isunique to A1 and N2 comprises a nucleotide sequence that is unique toA2. “n” in certain embodiments, is 0-15, 0-25, 0-50, 0-100, 0-150,0-250, 0-500, 0-1000, 0-2500, 0-5000, 0-10,000, 0-25,000, or 0-50,000amino acids. A unique sequence U may for example have a size from 10nucleotides to 500 nucleotides, from 20 to 400, from 30 to 300, from 40to 200, from 15 to 150, from 50 to 100, from 25 to 75, 45 to 65, or maybe around 20, around 30, around 40, around 50, around 60, around 70,around 80, around 90, or around 100 nucleotides. In certain embodiments,U has a size from 10-1000, 10-2500, 10-5000, 10-10,000, 10-25,000, or10-50,000 nucleotides. A unique sequence may differ from any otherunique sequence by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,16, 18, 19, 20 or more nucleotides. In certain embodiments, the uniquesequence differs from any other unique sequence by 25, 50, 75, 100, 250,500, 1000, 2500, 5000, 10,000, 20,000 or more nucleotides.

In certain embodiments, N comprises:

x_(n)P1-U-P2x_(n),

wherein x is any nucleotide, n is a number of nucleotides, P1 and P2 areprimer sequences, and U is a unique sequence. In certain embodiments,the primer sequences can be between 10 and 35 nucleotides long, e.g. 10,11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28,29, 30, 31, 32, 33, 34, or 35 nucleotides. In certain embodiments, theprimer sequences can be 10-40, 10-45, 10-50, 10-55, 10-60, 10-65, 10-70,10-75, 10-100, 10-250, 10-500, or 10-1000 nucleotides long. “n” incertain embodiments, is 0-15, 0-25, 0-50, 0-100, 0-150, 0-250, 0-500,0-1000, 0-2500, 0-5000, 0-10,000, 0-25,000, 0-50,000 or 0-100,000nucleotides.

In certain embodiments, a specific A, comprising either X_(n) orX_(n)Y[M]X_(n), is joined via a linker L with a specific N, comprisingx_(n)P1-U-P2x_(n). In certain embodiments, wherein U is unique, P1 andP2 are the same for every specific A.

For example, the following A segments may be joined via L with thefollowing N segments of A-L-N:

x_(na)Y₁[M₁]x_(na)-L-x_(nn)P1-U₁-P2x_(nn)

x_(na)Y₂-[M₂]x_(na)-L-x_(nn)P1-U₂-P2x_(nn)

x_(na)Y₃-[M₃]x_(na)-L-x_(nn)P1-U₃-P2x_(nn),

wherein “X” is an amino acid; “na” is a number of amino acids; Y₁, Y₂,Y₃ are different modified amino acids; M₁, M₂, M₃ are differentmodifications, wherein X_(na)Y₁[M₁]X_(na) is least 5 amino acids; “L” isa linker; “x” is any nucleotide, “nn” is a number of nucleotides, P1 andP2 are primer sequences, and U₁, U₂, U₃ are unique nucleotide sequences.In certain embodiments, the primer sequences P1 and P2 are independently10-35, 10-40, 10-45, 10-50, 10-55, 10-60, 10-65, 10-70, 10-75, 10-100,10-250, 10-500, or 10-1000 nucleotides long. “na” in certainembodiments, is 0-15, 0-25, 0-50, 0-100, 0-150, 0-250, 0-500, 0-1000,0-2500, 0-5000, 0-10,000, 0-25,000, or 0-50,000 amino acids. “nn” incertain embodiments, is 0-15, 0-25, 0-50, 0-100, 0-150, 0-250, 0-500,0-1000, 0-2500, 0-5000, 0-10,000, 0-25,000, 0-50,000 or 0-100,000nucleotides. In certain embodiments, U has a size from 10-25, 10-50,10-100, 10-250, 10-500, 10-1000, 10-2500, 10-5000, or 10-10,000nucleotides.

As will be apparent to one of skill in the art, by using the same primerpair (P1 and P2), N comprising the three unique sequences U₁, U₂, U₃ canbe sequenced. In this example, every specific U in N is linked to aspecific A, comprising a modified amino acid.

It should be appreciated that an amplification sequence, e.g. P1 and/orP2, is not always needed and/or not always desired. In certainembodiments, N comprises:

x_(n)Ux_(n),

wherein x is any nucleotide, n is a number of nucleotides and U is aunique sequence. “n” in certain embodiments, is 0-15, 0-25, 0-50, 0-100,0-150, 0-250, 0-500, 0-1000, 0-2500, 0-5000, 0-10,000, 0-25,000,0-50,000 or 0-100,000 nucleotides. In certain embodiments, U has a sizefrom 10-25, 10-50, 10-100, 10-250, 10-500, 10-1000, 10-2500, 10-5000, or10-10,000 nucleotides.

For example, certain sequencing and microarray approaches interrogatewhole samples by incorporating all DNA into a library. These methods maybe “amplification-free” (as described for example by Kozarewa et al.“Amplification-free Illumina sequencing-library preparation facilitatesimproved mapping and assembly of (G+C)-biased genomes” Nature Methods6:291-295 (2009); Meyer and Kircher “Illumina sequencing librarypreparation for highly multiplexed target capture and sequencing” ColdSpring Harb Protoc. 2010(6):pdb.prot5448 (2010). Amplification-freemethods may be used reduce or avoid sampling biases during librarypreparation that can result in libraries that are lower in complexitythan the genomic DNA from which they were derived. For such uses, N maycomprise a unique sequence U of an appropriate length that is compatiblewith the specific procedure. In certain embodiments, N comprisesx_(n)Ux_(n) of a length appropriate to be incorporated into the libraryand/or N comprises x_(n)Ux_(n) which is capable of hybridization tospecific oligonucleotides, such as oligonucleotides immobilized on achip or a flow cell. The specific length requirement may vary betweenmethods. In certain embodiments, x_(n)Ux_(n) has a length ofapproximately 100, 200, 300, 400, or 500 nucleotides. In certainembodiments, x_(n)Ux_(n) has a length between 50-150, 100-200, 150-250,200-300, 250-350, 300-400, 350-450, or 400-500 nucleotides. In certainembodiments, x_(n)Ux_(n) has a length between 10-25, 10-50, 10-100,10-250, 10-500, 10-1000, 10-2500, 10-5000, 10-10,000, 10-25,000,10-50,000, 10-100,000 or more nucleotides.

“L” as used herein is a linker. In certain embodiments, L is a chemicallinker. The linker L associating polypeptide A with oligonucleotide Nmay be any chemical moiety capable of associating the two segments A andN. This linker can have any length or other characteristic and minimallycomprises two reactive terminal groups that can chemically interact with(and covalently bind to) the two segments A and N. The linker may be assimple as a covalent bond, or it may be a polymeric linker many atoms inlength (e.g., polyethylene, polyethylene glycol, polyamide, polyester,etc.). In certain embodiments, linker L is 1-10 atoms, 1-25 atoms, 1-50atoms, 1-100 atoms, 1-200 atoms, 1-500, 1-1000, 1-5000, 1-10,000,1-50,000 or 1-100,000 atoms in length. In certain embodiments, thelinker is a covalent bond (e.g., a carbon-carbon bond, disulfide bond,carbon-heteroatom bond, etc.). The linker may included functionalizedmoieties to facilitate attachment of a nucleophile (e.g., thiol, amino)from the polypeptide segment A to the linker L. Any electrophile may beused as part of the linker. Exemplary electrophiles include, but are notlimited to, activated esters, activated amides, Michael acceptors, alkylhalides, aryl halides, acyl halides, and isothiocyanates.

In certain embodiments, L is a heterobifunctional linker. In certainembodiments, N is modified to comprise one or more primary amines orthiols attached to specific bases of the nucleotides. After modificationof the one or more bases in N, amine- or sulfhydryl-reactivecrosslinkers can be used for their conjugation to A.

Another functional group that can be chemically modified to allow thecoupling of polypeptide A to oligonucleotide N is the 5′-phosphategroup. Using the 5′ end of oligonucleotide N as the conjugation point byattaching a 5′-phosphate group has an advantage of keeping the remainderof the nucleic acid sequence unmodified and free to interact or easilyhybridize to a complementary target (for example a primer). The alkylphosphate may, for example, be reactive with the water-solublecarbodiimide EDC (Pierce, Rockford, Ill.), which forms a phosphateester. Subsequent coupling to the amine-containing A segment can beperformed to form a stable phosphoramidate linkage.1-Ethyl-3-[3-dimethylaminopropyl]carbodiimide hydrochloride (EDC orEDAC) is a zero-length crosslinking agent used to couple carboxyl groupsto primary amines. EDC reacts with a carboxyl to form an amine-reactiveO-acylisourea intermediate. If this intermediate does not encounter anamine, it will hydrolyze and regenerate the carboxyl group. In thepresence of N-hydroxysulfosuccinimide (Sulfo-NHS), EDC can be used toconvert carboxyl groups to amine-reactive Sulfo-NHS esters. This is forexample, accomplished by mixing the EDC with a carboxyl containingmolecule and adding Sulfo-NHS.

If a diamine molecule is used to modify the DNA 5′-phosphate, then theresultant amine-modified oligonucleotide N can be coupled to the Asegment using a heterobifunctional reagent. For example, using a diaminecompound that contains a disulfide (e.g., cystamine) and then reducingthe disulfide group results in a sulfhydryl that may be conjugated withA segments rendered sulfhydryl-reactive (e.g., maleimide-activated)using the heterobifunctional reagent Sulfo-SMCC (Pierce, Rockford,Ill.). Sulfosuccinimidyl-4-(N-maleimidomethyl)cyclohexane-1-carboxylate(Sulfo-SMCC) is a water-soluble, non-cleavable and membrane impermeablecrosslinker. It contains an amine-reactive N-hydroxysuccinimide (NHSester) and a sulfhydryl-reactive maleimide group. NHS esters react withprimary amines at pH 7-9 to form stable amide bonds. Maleimides reactwith sulfhydryl groups at pH 6.5-7.5 to form stable thioether bonds. Themaleimide groups of Sulfo-SMCC and SMCC are unusually stable up to pH7.5 because of the cyclohexane bridge in the spacer arm.

Alternatively, N may be biotinylated, using e.g. photoreactive reagents.Photoactivatable biotin (Pierce, Rockford, Ill.) may be used thatcomprises a phenyl azide group at the end of a spacer arm and the biotingroup at the other end, which allows the biotin to be non-selectivelyinserted into the nucleic acid structure e.g. by photolyzing.

Other methods and reagents for coupling the oligonucleotide segment N tothe polypeptide segment A are well known in the art, described forexample in Nitta et al., FEBS 166(1):194-198 (1984).

Polypeptide-Oligonucleotide Conjugates as Controls forImmuno-Precipitations of Non-Histone Proteins:

It would be appreciated by one of skill in the art that thepolypeptide-oligonucleotide conjugates of the general formula A-L-Nprovided herein are also suitable for generating controls and/orinternal standards for immuno-precipitation assays of non-histoneproteins. In certain embodiments, polypeptide-oligonucleotide conjugatesdescribed herein are provided as internal standards for antibodiesraised against non-histone proteins. In certain embodiments, thepolypeptide-oligonucleotide conjugates are provided as internalstandards for antibodies specific for amino acid mutations of thenon-histone polypeptide of interest, e.g. point mutations, antibodiesspecific for post-translational modifications of the non-histonepolypeptide of interest, or antibodies designed to distinguish betweensimilar epitopes.

Non-histone proteins can be for example DNA-binding proteins orchromatin-associated factors, such as transcription factors, cofactorsof activator or repressor complexes, chromatin-modifying enzymes, e.g.histone acetylases, histone deacetylases, methylases, demethylases,replication factors, repair factors, etc. DNA-binding proteins orchromatin-associated factors include, but are not limited to, ASH1L,ASH2, ATF2, ASXL1, BAP1, bc110, Bmi1, BRG1, CARM1, KAT3A/CBP, CDC73,CHD1, CHD2, CTCF, DNMT1, DOTL1, EHMT1, ESET, EZH1, EZH2, FBXL10,FRP(Plu-1), HDAC1, HDAC2, HMGA1, hnRNPA1, hp1 gamma, Hset1b, Jarid1A,Jarid1C, KIAA1718_JHDM1D, KAT5, KMT4, LSD1, NFKB P100, NSD2, MBD2, MBD3,MLL2, MLL4, P300, pRB, RbAP46/48, RBP1, RbBP5, RING1B, RNApolII P S2,RNApolII P S5, ROC1, sap30, setDB1, Sf3b1, SIRT1, Sirt6, SMYD1, SP1,SUV39H1, SUZ12, TCF4, TET1, TRRAP, TRX2, WDR5, WDR77, YY1. Commercialantibodies are available for all of these factors.

Specific posttranscriptional modifications include but are not limitedto phosphorylation, acetylation, and ubiquitination. For example, thepolypeptide-oligonucleotide conjugates may serve as controls forp53-specific modifications, such as phospho-serine 6, phospho-threonine18, acetyl-lysine 373, acetyl-lysine 382, phosphor-serine 392, orpRB-specific modifications, such as phospho-serine 601, phospho-serine605, phospho-serine 773, acetyl-873, and acetyl-874. Such controls maybe generated according to the teachings provided herein. Thepolypeptide-oligonucleotide conjugates of the general formula A-L-N maycomprise A comprising X_(n)Y[M]X_(n) and N comprising x_(n)P1-U-P2x_(n)or x_(n)Ux_(n) as described herein. Non-limiting examples for A of p53modification-specific controls are: X_(n)S[ph]X_(n), X_(n)T[ph]X_(n),and X_(n)K[ac]X_(n), wherein X is any amino acid, preferably an aminoacid derived from p53 amino acid sequence. For example, A specific forhuman p53 phospho-serine 6 may comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more amino acids of the humanp53 amino acid sequence, such as

(SEQ ID NO: 60) MEEPQS[ph]DPSV EPPLSQETFS DLWKLLPENN, (SEQ ID NO: 61)PQS[ph]DPS, (SEQ ID NO: 62) QS[ph]DPSV EPPLSQ, and (SEQ ID NO: 63)MEEPQS[ph]D.A specific for human p53 acetyl-lysine 373, may comprise 1, 2, 3, 4, 5,6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more aminoacids of the human p53 amino acid sequence, such as

(SEQ ID NO: 64) GSRAHSSHLK SKK[ac]GQSTSRH KKLMFKTEGP DSD,(SEQ ID NO: 65) SKK[ac]GQ, (SEQ ID NO: 66) HLK SKK[ac]GQSTSRH, and(SEQ ID NO: 67) K[ac]G.A specific for human pRb acetyl-873, and acetyl-874, may comprise 1, 2,3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or moreamino acids of the human pRb amino acid sequence, such as

(SEQ ID NO: 68) TSEKFQKINQ MVCNSDRVLK RSAEGSNPPK PLK[ac]K[ac]LRFDIEGSDEADGSKH LPGESKFQQK, (SEQ ID NO: 69) PLK[ac]K[ac]LRFD, and(SEQ ID NO: 70) PPK PLK[ac]K[ac]LRFDIE GSDEADGS.

In certain embodiments, A comprises more than 20 amino acids of theDNA-binding protein or chromatin-associated factor that may comprise aspecific amino acid modification. In certain embodiments, A comprises is25, 50, 75, 100, 250, 500, 1000, 2500, 5000, 10,000, 25,000, or 50,000amino acids of the DNA-binding protein, chromatin-associated factor orprotein complexes thereof (e.g. multi-subunit comprisingchromatin-remodeling complexes). In certain embodiments, A comprises theamino acids of the full-length DNA-binding protein orchromatin-associated factor.

As described herein, N may comprise a unique sequence and primersequences, e.g. x_(n)P1-U-P2x_(n), wherein the unique sequence may beused to identify the specific amino acid modification represented in A.In certain embodiments, N does not comprise an amplification sequence(e.g. P1 and P2) and comprises a unique sequence x_(n)Ux_(n) that may beused to identify the specific amino acid modification represented in A.One of ordinary skill would appreciate that polypeptide-oligonucleotideconjugates may be generated that represent specific posttranscriptionalmodifications or specific mutations for any polypeptide of interest forwhich such modifications and/or mutations are known.

For many of the commercially available antibodies specific forDNA-binding proteins or chromatin-associated factors their suitabilityin immuno-precipitation assays is unknown. Controls and internalstandards that could be used to test the suitability of such antibodiesare generally not available. Using existing controls is often costly andtime consuming because data about the genomic regions that are bound bythe DNA-binding proteins and chromatin-associated factors is not alwaysavailable. Such lack of information requires the generation of multipleprimers specific for different genomic regions and/or requiresperforming ChIP-Seq assays. To overcome these limitations, thepolypeptide-oligonucleotide conjugates described herein may be used asinternal standards for any experiment involving antibodies specific fornon-histone proteins, such as DNA-binding proteins andchromatin-associated factors. In certain embodiments, thepolypeptide-oligonucleotide conjugates described herein may be used forimmuno-precipitation experiments. In other embodiments, thepolypeptide-oligonucleotide conjugates described herein may be used asinternal standards for comparing and/or using data obtained from anytype of suitable assay or experiment in combination with data obtainedfrom ChIP, e.g. when using antibodies specific for DNA-binding proteinsand chromatin-associated factors. The polypeptide-oligonucleotideconjugates described herein may be used as internal standards fornormalization purposes (as described herein), for example, whenmeasuring the effect of a gene “knock-down” on a cell (such as by anantisense or RNAi-mediated knock-down, by a knock-out mutation, or by amisregulated cellular pathway) and comparing the ChIP data obtained fromthe knock-down cell with the ChIP data obtained from a wild-type cell.It would be understood by one of ordinary skill that thepolypeptide-oligonucleotide conjugates described herein may be used incircumstances not involving knock-down, such as, for example, incircumstances when a DNA-binding protein and chromatin-associated factoris modified differently (e.g. post-transcriptionally modified) in anytwo cells. The two cells may be of different cell type, the same celltype but derived from different tissue or from a different species, ormay be derived from a wild-type and a mutant cell (e.g. a normalcell/cancer cell pair).

Polypeptide/Polynucleotide-Oligonucleotide Conjugates as Controls forImmuno-Precipitations of Non-Histone Proteins:

Other aspects of the invention relate to control agents forimmuno-precipitation (IP) assays, including but not limited to RNA-IPfollowed by sequencing (RIP-seq), methylated-DNA IP followed bysequencing (mDIP-seq), bisulphite sequencing (BS-seq), High-throughputsequencing of RNA isolated by crosslinking IP (HITS-CLIP),formaldehyde-assisted isolation of regulatory elements followed bysequencing (FAIRE-seq), and micrococcal nuclease digestion followed bysequencing (MNase-seq). Control agents provided herein comprise theformula:

X-B or B-X,

where X is a molecule (e.g., polypeptide, such as A described above, ora polynucleotide), and B (also referred to as “barcode”) is anoligonucleotide (e.g., DNA or RNA) comprising, for example, 10nucleotides, wherein the sequence of nucleotides of B uniquelyidentifies X. In some configurations, a linker L is used to conjugate Band X. Examples of control agents include, but are not limited to,barcoded DNA-peptide conjugates, barcoded RNA-peptide conjugates,barcoded methylated DNA oligos, and assembled nucleosomes conjugated tobarcoded DNA.

Polypeptide-Oligonucleotide Conjugates as Validation Tools for ScreeningChIP-Capable Antibodies:

For ChIP assays, it is advantageous to fully characterize the antibodiesused in the assay. Antibodies used in ChIP assays typically recognizehistones, histone modifications or chromatin-associated factors. Onecommon method of characterizing antibody specificity (epitoperecognition) employs assays involving peptide competition (using targetand non-target antigens as competitors) in both ELISA and Western blot.Western blotting can also be used to demonstrate that the correct targethas been successfully immuno-precipitated. Calf thymus histonepreparations are often used as a positive control histone sample forvalidating antibody specificity in Western blot. Immunofluorescence canbe used to validate that antigen recognition occurs in a cellularcontext, and can also be combined with competition assays.

However, even full characterization will not necessarily providesufficient information about the antibody's suitability for, andspecificity in ChIP, as the effects of cross-linking can significantlyalter (native) epitopes and/or may lead to the loss of specificepitopes. Further, the binding affinity of certain may decreasedramatically under more stringent buffer conditions (that are commonlyused in ChIP assays, e.g. high salt and/or detergent conditions) thatincrease antibody specificity.

Specific antibodies for ChIP should be affinity-purified, e.g. when theantibody is a monoclonal antibody (raised against a specific epitope).Many laboratories use sera (e.g. polyclonal antibody population thatrecognize different epitopes) as their antibody source and inherentbackground problems are overcome by using highly stringent buffers.

A stringent test for the suitability of an antibody for ChIP is toperform parallel ChIP assays in wild-type and mutant or modified andunmodified backgrounds to demonstrate that the observed enrichment isdue solely to the target antigen. Such tests are difficult to performwith the controls that are currently available.

The polypeptide-oligonucleotide conjugates of the general formula A-L-Nthat may comprise A comprising X_(n)Y[M]X_(n) and N comprisingx_(n)P1-U-P2x_(n) or x_(n)Ux_(n) as described herein may be used toprovide specific epitopes to screen novel and/or untested antibodies fortheir suitability in ChIP assays. For example, a pool (library) of thepolypeptide-oligonucleotide conjugates provided herein specific fordifferent histone modifications may be used in a mock-ChIP assay, underconditions similar or identical to those actually used in a ChIP assayusing genomic material, to screen and/or validate antibodies for theirspecificity and/or affinity to specific histone modifications. Such apool may comprise polypeptide-oligonucleotide conjugates of the generalformula A-L-N comprising A segments that comprise antigens representingmono-methylated H3K4, mono-methylated H3K9, mono-methylated H3K27,mono-methylated H3K79, di-methylated H3K79, tri-methylated H3K4,acetylated H3K9, acetylated H3K14, tri-methylated H3K9 andtri-methylated H3K27. An antibody may be screened for suitability in aChIP assay using such pool (library) by contacting the antibody with thepolypeptide-oligonucleotide conjugate pool under conditions similar oridentical to those actually used in a ChIP assay using genomic material.If the antibody is for example specific for mono-methylated H3K9, asubsequent sequence analysis and quantification of the precipitatedfraction (e.g. by qPCR) would produce a statistically significantoverrepresentation of the unique nucleotide sequence (of N) that islinked via the linker L to the A segment comprising the antigenrepresenting mono-methylated H3K9. All other unique sequences linked tothe A segments comprising the antigens representing the other histonemodifications would be underrepresented in a statistically significantmanner. Antibodies with low affinity and/or low specificity may producesignals that are not statistically significant, e.g. over background orover the signal derived from the other polypeptide-oligonucleotideconjugates representing the non-desired antigens.

Provided herein are thus screening methods using thepolypeptide-oligonucleotide conjugates described herein to screenantibodies for their suitability in ChIP assays, wherein antibodies thatproduce a significant overrepresentation of a signal specific to asingle amino acid modification or specific to a combination of histonemodifications in conditions similar or identical to those actually usedin a ChIP assay using genomic material are considered suitable for usein ChIP assays.

It would be appreciated by one of ordinary skill that the use of thepolypeptide-oligonucleotide conjugates described herein to screenantibodies is not limited to ChIP assays and histone modifications. Thepolypeptide-oligonucleotide conjugates described herein may be used toscreen antibodies for suitability in immuno-precipitation assays of anynon-histone polypeptide, for example using A segments comprisingantigens representing specific post-translational modification (e.g.phosphorylation, acetylation, ubiquitination, etc.) of the non-histonepolypeptide of interest or antigens representing one or more specificpoint mutation(s) within the amino acid sequence of the non-histonepolypeptide of interest and/or the appropriate antigen representing thenon-modified and non-mutated forms.

Use of Polypeptide-Oligonucleotide Conjugates to Normalize ChIP andOther Assay Data and to Quantify Experimental Parameters of ChIP Assays:

Variations in the starting material (quantity and/or quality) in ChIPassays are possible. ChIP data may therefore be normalized for theamount of starting material, e.g. to avoid errors introduced due touneven sample quantities. To normalize the data obtained, the finalamplification value may be divided by the amplification value of inputmaterial. For example, one may take a sample of the lysed startingmaterial for PCR of control regions in parallel with the eluted materialfrom the ChIP assay. It is possible that certain regions of the genomeare precipitated more effectively or amplify better than others.Further, there is the possibility of nucleosome rearrangement duringfragmentation (e.g. enzymatic fragmentation). PCR primers may thereforebe generated specific for several regions in the starting material, aswell as for the purified/immuno-precipitated material, as controls.Normalization is also difficult in microarray and sequencing assays.Such assays could also be improved by providing internal standards, suchas the agents provided herein.

The polypeptide-oligonucleotide conjugates of the general formula A-L-Nthat may comprise A comprising X_(n)Y[M]X_(n) and N comprisingx_(n)P1-U-P2x_(n) or x_(n)Ux_(n) as described herein may be used toprovide quantifiable controls and/or internal standards. Thepolypeptide-oligonucleotide conjugates described herein may be providedas a pool in which the concentration of each individualpolypeptide-oligonucleotide conjugate is accurately known orindividually at a known concentration. For example, a pool of or anindividual polypeptide-oligonucleotide conjugate(s) of knownconcentration may be used as an input control, as a process controlwithout genomic sample material and/or may be “spiked” into the samplesof fragmented genomic material. The starting concentration of thepolypeptide-oligonucleotide conjugate(s) in each case is known or can becalculated. The polypeptide-oligonucleotide conjugates that may compriseA comprising X_(n)Y[M]X_(n) and N comprising x_(n)P1-U-P2x_(n) provide asignal amplification of the unique nucleic acid sequence U that isindependent of variations in chromatin, since U may be designed in suchway that it is of one particular length (e.g. 10, 20, 30, 40, 50, ormore nucleotides) that is the same for each unique sequence U and P1 andP2 may be the same sequence(s) for each polypeptide-oligonucleotideconjugate. In certain embodiments, N does not comprise an amplificationsequence (e.g. P1 and P2) and comprises a unique sequence x_(n)Ux_(n).The magnitude of the signal obtained (e.g. from qPCR, hybridization,sequencing or other quantification method) for the immuno-precipitatedpolypeptide-oligonucleotide conjugates may then depend only on theconditions used for the ChIP assay and on the specificity and/oraffinity of the antibody for the antigen (X_(n)Y[M]X_(n)) represented bythe A segment. To normalize the signal obtained for theimmuno-precipitated polypeptide-oligonucleotide conjugates, the finalamplification value may be divided by the amplification value of inputpolypeptide-oligonucleotide conjugates. Provided herein are thus methodsfor quantifying one or more experimental parameters of ChIP assays usingthe polypeptide-oligonucleotide conjugates described herein. Suchexperimental parameters include but are not limited to, sample loss,immuno-precipitation efficiency, quality of the starting/input material(e.g. fragmented genomic material), relative fold enrichment of theantigen-specific signal for the immuno-precipitated sample. Providedherein are also methods of normalizing the signal obtained for theimmuno-precipitated genomic material using thepolypeptide-oligonucleotide conjugates described herein.

Kits Comprising Polypeptide-Oligonucleotide Conjugates for ChIP Assays:

Provided herein are kits for chromatin immuno-precipitation (ChIP)assays. In certain embodiments, such kits comprise thepolypeptide-oligonucleotide conjugates of the formula A-L-N, asdescribed herein, and one or more other chemical reagents necessary toperform a ChIP assay and/or chemical reagents necessary to performsubsequent analysis, e.g. PCR, hybridization, or sequencing. Such kitsmay contain one or more enzymes necessary to perform the ChIP assay, forexample, RNaseA and Proteinase K; one or more solutions and buffers,such as, formaldehyde, glycine, PBS, cell lysis buffer, Triton X-100,protease inhibitor cocktails, wash buffers elution buffers; antibodies(specific and control); and hardware, such as magnetic beads andmulti-well plates. Such kits may contain one or more enzymes necessaryto perform chromatin fragment modification (e.g. addition of adapters)and subsequent Real Time PCR or sequencing, for example, Klenow DNApolymerase, DNA polymerase, T4 ligase, T4 polynucleotide kinase, T4 DNApolymerase, Klenow fragment 3′ to 5′ exo minus; one or more solutionsand buffers, such as, enzyme reaction buffers, dATP, dNTPs, ultrapurewater, TE; PCR or sequencing specific adapters, PCR or sequencingprimers; and hardware, such as e.g. DNA purification columns andmulti-well plates. In certain embodiments, kits may be providedcomprising one or more polypeptide-oligonucleotide conjugates of theformula A-L-N, as described herein, specific for one or more particularChIP targets, e.g. histone modifications, unmodified histones, orchromatin-associated factors (transcription factors, histone acetylases,histone deacetylases, methylases, demethylases, repressor/activatorco-factors, polymerases, DNA repair enzymes, etc.). In certainembodiments, a pool of 1, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60,65, 70, 75, 80, 85, 90, 95, 100 or more differentpolypeptide-oligonucleotide conjugates of the formula A-L-N may beprovided. For example, a pool may comprise one or morepolypeptide-oligonucleotide conjugates

X_(na)Y_(1, 2, 3, . . . z)[M_(1, 2, 3, . . . z)]X_(na)-L-x_(nn)P1-U_(1, 2, 3, . . . z)-P2x_(nn),

wherein “X” is an amino acid; “na” is a number of amino acids; Y₁, Y₂,Y_(3 . . . z) are “z” number of different modified amino acids; M₁, M₂,M_(3 . . . z) are “z” number of different modifications; “L” is alinker; “x” is any nucleotide, “nn” is a number of nucleotides, P1 andP2 are primer sequences, and U₁, U₂, U_(3 . . . z) are “z” number ofunique nucleotide sequences of, wherein “z” is the number of differentpolypeptide-oligonucleotide conjugates in the pool, e.g. 1, 5, 10, 15,20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 ormore. In certain embodiments, the primer sequences P1 and P2 areindependently 10-35, 10-40, 10-45, 10-50, 10-55, 10-60, 10-65, 10-70,10-75, 10-100, 10-250, 10-500, or 10-1000 nucleotides long. “na” incertain embodiments, is 0-15, 0-25, 0-50, 0-100, 0-150, 0-250, 0-500,0-1000, 0-2500, 0-5000, 0-10,000, 0-25,000, or 0-50,000 amino acids.“nn” in certain embodiments, is 0-15, 0-25, 0-50, 0-100, 0-150, 0-250,0-500, 0-1000, 0-2500, 0-5000, 0-10,000, 0-25,000, 0-50,000, 0-100,000nucleotides. In certain embodiments, U has a size from 10-25, 10-50,10-100, 10-250, 10-500, 10-1000, 10-2500, 10-5000, or 10-10,000nucleotides. In certain embodiments, N does not comprise anamplification sequence (e.g. P1 and P2) and comprises a unique sequencex_(n)Ux_(n).

The pools of polypeptide-oligonucleotide conjugates may represent 1, 5,10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95,100 or more different histone modifications, including but not limitedto

1) modifications for Histone H1, such as H1 (phospho S1+T3), H1 (phosphoS35), H1 (acetyl K63);

2) modifications for Histone H2A, such as H2A (asymmetric di methyl R3),H2A (symmetric di methyl R3), H2A (acetyl K5), H2A (mono methyl R17),H2A (symmetric di methyl R77), H2A (Hydroxy P26), H2A (mono methylK125), H2A (tri methyl K125), H2A (mono methyl K127), H2A (tri methylK127), H2A (phospho S129);

3) modifications for Histone H2B, such as H2B (acetyl K5), H2B (dimethyl K5), H2B (Hydroxy P10), H2B (di methyl K43);

4) modifications for Histone H3, such as H3 (mono methyl R2), H3(citrulline 2+8+17), H3 (mono methyl K4), H3 (di methyl K4), H3 (trimethyl K4), H3 (di+tri methyl K4), H3 (acetyl K9), H3 (acetyl K9,phospho S10), H3 (mono methyl K9), H3 (di methyl K9), H3 (tri methylK9), H3 (phospho S10), H3 (asymmetric di methyl R17), H3 (acetyl K18),H3 (acetyl K27), H3 (di methyl K27), H3 (tri methyl K27), H3 (monomethyl K27, tri methyl K27+K4), H3 (mono methyl K36), H3 (tri methylK36), H3 (Hydroxy P38), H3 (mono methyl K79), H3 (di methyl K79), H3(tri methyl K79), H3 (mono+di+tri methyl K79), H3 (Hydroxy P121), H3(tri methyl K122); and

5) modifications for Histone H4, such as H4 (symmetric di methyl R3), H4(acetyl K8), H4 (acetyl K12), H4 (mono methyl K20), H4 (tri methyl K20),H4 (phospho T30), H4 (Hydroxy P32), H4 (tri methyl K59), H4 (phosphoT80), H4 (acetyl K91), H4 (phospho T96).

It should be appreciated that kits comprisingpolypeptide-oligonucleotide conjugates comprising A segments thatcomprise antigens of non-histone polypeptides, as described herein, mayalso be provided. Such kits may comprise pools ofpolypeptide-oligonucleotide conjugates comprising A segments thatcomprise antigens of, for example, p53-specific post-translationalmodifications, e.g. phosphorylated Ser 6, Ser 9, Ser 15, Thr 18, Ser 20,Ser 33, Ser 37, Ser 46, Thr 55, Thr 155, Ser 315, and/or Ser 392.

Pools of polypeptide-oligonucleotide conjugates may be providedindividually that is without any other reagent, e.g. as an accessory forChIP assays, or may be provided together with agents necessary toperform ChIP assays (e.g. antibodies, cross-linking, binding, washing,elution buffers, etc.) and/or subsequent with agents necessary toperform subsequent assays of nucleic acid analyses (e.g. PCRamplification, sequencing, hybridization, etc.) as depicted in FIG. 4.The polypeptide-oligonucleotide conjugates may be provided lyophilizedor in suspension (e.g. in a suitable buffer). If thepolypeptide-oligonucleotide conjugates are provided in lyophilized form,a suitable suspension buffer may also be provided with the kit.

The polypeptide-oligonucleotide conjugates may be used in any ChIPassay. ChIP assays may be used to analyze the spatial and temporaldynamics and interactions of chromatin and its associated factors, whichcan be, for example, detected at a single promoter or over the entirehuman genome. ChIP assays are based on the selective enrichment of achromatin fraction containing a specific antigen. Antibodies thatrecognize a protein (e.g. a chromatin-associated factor such as atranscription factor) or protein modification (e.g. a histone tailmodification) of interest can be used to determine the relativeabundance of that antigen at one or more locations (loci) in the genome.It is more common to analyze euchromatin, which is though to containactive genes and to maintain an “open” and “extended” chromatin.Heterochromatin, which is thought to contain many inactive genes andrepetitive DNA sequences and is thought to be in a “condensed” state isgenerally more difficult to analyze by ChIP.

Generally, ChIP assays can be used to determine whether a given proteinbinds to a specific location on the chromatin in vivo or if a specifichistone modification is present at a specific location on the chromatinat the time of analysis. ChIP may be used to selectively enrich for DNAsequences bound by a particular protein (e.g. transcription factor orhistone) in living cells by cross-linking DNA-protein complexes andusing an antibody that is specific against a protein of interest.Specific ChIP protocols are well known in the art. The ChIP proceduremay consists of the following steps:

-   -   (a) (optionally) cross-linking of chromatin in vivo (to        immobilize the antigen of interest to its chromatin binding        site)    -   (b) isolation of total chromatin    -   (c) fragmentation of the chromatin isolated in (b)    -   (d) immunoprecipitation of the chromatin fragments obtained in        (c)    -   (e) analysis of the immunoprecipitated fraction obtained in (d)        to determine the amount of a target DNA sequence relative to its        abundance in the input chromatin.

The quantitative analysis is typically carried out using PCR, sequencingor hybridization-based techniques. Such procedures are well now in theart and, for example, Allis & Wu ((Eds). (2004) “Chromatin and chromatinremodelling enzymes”, Methods in Enzymology v376, Elsevier AcademicPress, 2004) provide a review of the procedures and methodologies ofChIP.

The polypeptide-oligonucleotide conjugates described herein may comprisean N segment comprising x_(n)P1-U-P2x_(n). It may therefore beparticularly useful to modify the immuno-precipitated genomic fractionobtained through the ChIP assay in such way as to link nucleotides ofthe sequence of P1 and P2 to the obtained nucleic acid fragments. Thismay allow amplification and/or quantification using the same primers forthe control (e.g. the polypeptide-oligonucleotide conjugates describedherein) and the immuno-precipitated genomic material. Use of the sameprimers may reduce or eliminate unwanted variations in signal obtainedin the amplification and/or quantification assays. In certainembodiments, N does not comprise an amplification sequence (e.g. P1 andP2) and comprises a unique sequence x_(n)Ux_(n).

Generally, to analyze the immunoprecipitated fraction of fragmentedchromatin (genomic DNA), the DNA fragments may be eluted and purified(e.g. by phenol/chloroform extraction-ethanol precipitation or affinitypurification using silica beads, such as QIAgen (Germantown, Md.) DNApurification kits: e.g. QIAquick™ column) and may be further modified toallow amplification and/or sequencing (e.g. from the same primers P1 andP2 provided in the polypeptide-oligonucleotide conjugates describedherein). Common modification steps include:

(a) performing end repair: to convert the overhangs resulting fromfragmentation into blunt ends, using e.g. T4 DNA polymerase and E. coliDNA polymerase I Klenow fragment. The 3′ to 5′ exonuclease activity ofthese enzymes removes 3′ overhangs and the polymerase activity fills inthe 5′ overhangs,

(b) addition of ‘A’ bases to the 3′ end of the DNA fragments: to add an‘A’ base to the 3′ end of the blunt phosphorylated DNA fragments, usingthe polymerase activity of e.g. Klenow fragment (3′ to 5′ exo minus).This may be performed to prepare the DNA fragments for ligation toadapters that have a single ‘T’ base overhang at their 3′ end,

(c) ligation of adapters to DNA fragments, e.g. using DNA ligase

(d) purification of ligation products: to remove any unligated adaptersor any adapters that may have ligated to one another, using e.g. gelpurification,

(e) enrichment of the adapter-modified DNA fragments by PCR: toselectively enrich DNA fragments that have adapter molecules on bothends and to amplify the amount of DNA,

(f) validation and analysis of the obtained library.

For validation and analysis chromatin immunoprecipitation-massivelyparallel DNA sequencing (ChIP-Seq) may be used. It can be used toprecisely map global DNA binding sites for any protein of interest, e.g.transcription factor, restriction enzyme, or other chromatin associatedproteins, on a genome scale. ChIP-DNA fragments are sequencedsimultaneously using a genome sequencer. A single sequencing run canscan for genome-wide associations with high resolution. Massivelyparallel sequence analyses may be used in conjunction with whole-genomesequence databases to analyze the interaction pattern of a protein ofinterest (e.g. transcription factors, polymerases or transcriptionalmachinery) with DNA (Johnson et al. (2007) Science 316: 1497-1502), orto analyze the pattern of an epigenetic chromatin modification ofinterest (e.g. histone modifications or DNA modifications). Massivelyparallel sequencing is known in the art and many sequencing methods maybe used. Some technologies may use cluster amplification ofadapter-ligated ChIP DNA fragments on a solid flow cell substrate. Theresulting high density array of template clusters on the flow cellsurface may then be submitted to sequencing-by-synthesis in parallelusing for example fluorescently labeled reversible terminatornucleotides. Templates are sequenced base-by-base during each read. Theresulting data may be analyzed using data collection and analysissoftware that aligns sample sequences to a known genomic sequence.

Chromatin immunoprecipitation may also be combined with microarray“ChIP-on-chip,” which requires a hybridization array. ChIP-on-chip mayrequire large sets of tiling arrays (of overlapping probes designed todensely represent a genomic region of interest). Tiling arrays that maybe used with the polypeptide-oligonucleotide conjugates described hereinmay comprise oligonucleotides comprising a sequence to which N is atleast in part complementary. These complementary sequences may be of alength sufficient to allow specific hybridization between parts or allof the nucleotide sequence provided by N and the oligonucleotide on thetiling array. In certain embodiments, wherein N comprises x_(n)Ux_(n),all or parts of the unique sequence U is complementary to theoligonucleotide on the tiling array. The polypeptide-oligonucleotideconjugates described herein may then be quantified using such tilingarrays. Upon acquisition of data (readout), for example by sequencing orhybridization, the relative representation of the differentpolypeptide-oligonucleotide conjugates described herein may be evaluatedby comparing their representation a) within a given sample and/or b)with a control sample(s). Enrichment ratios may then be calculated foreach polypeptide-oligonucleotide conjugate. These ratios may then beused to estimate or calculate the degree to which the correspondingantigen (represented by the polypeptide-oligonucleotide conjugate) wasenriched by the immuno-precipitation assay and thereby evaluating theefficacy of the experiment in quantitative terms, such as, for example,sensitivity and/or specificity.

Additional Embodiments

Also contemplated herein are other control agents for otherimmuno-precipitation (IP) assays, as set forth below. An internalstandard for a particular IP assay may have the formula:

X-B or B-X,

where X is a molecule (e.g., polypeptide, such as A described above, ora polynucleotide), and B (also referred to as “barcode”) is anoligonucleotide (e.g., DNA or RNA) comprising, for example, 10nucleotides, wherein the sequence of nucleotides of B uniquelyidentifies X. In some configurations, a linker L is used to conjugate Band X.

RNA Immuno Precipitation (RIP)-RNA-Sequencing (RNA-Seq) (RIP-Seq)

In some embodiments, the internal controls described herein may be usedin RIP-seq assays. RIP is similar to ChIP described above, except ratherthan targeting DNA binding proteins as in ChIP, RIP targets RNA bindingproteins. In some embodiments, live cells may be lysed and theimmunoprecipitation can be performed with an antibody that targets aprotein of interest. By isolating the protein, the RNA will also beisolated as it is bound to the protein. In some embodiments, thepurified RNA-protein complexes can be separated by performing an RNAextraction and the identity of the RNA can be determined by cDNAsequencing (RNA-seq) or RT-PCR. In certain embodiments, some variants ofRIP, such as PAR-CLIP include cross-linking steps, which then mayrequire less careful lysis conditions. Internal controls for use with anRIP-seq assay include barcoded RNA-peptide conjugates, for example,having the configuration X-B, where X is an RNA-binding protein, and Bis an oligonucleotide of cDNA that uniquely identifies X.

Methylated-DNA Immuno Precipitation (meDIP or mDIP)-Sequencing

In some embodiments, the internal controls described herein may be usedin mDIP-sequencing. mDIP is a large-scale (chromosome- or genome-wide)technique that can be used to enrich for methylated DNA sequences. Incertain embodiments, the method comprises isolating methylated DNAfragments via an antibody raised against 5-methylcytosine (5mC). In someembodiments, a purified fraction of methylated DNA can be input tohigh-throughput DNA detection methods such as high-resolution DNAmicroarrays (MeDIP-chip) or next-generation sequencing (MeDIP-seq).Internal controls for use with an MeDIP-seq assay include barcodedmethylated DNA oligonucleotides, for example, having the configurationX-B, where X is a methylated DNA oligonucleotide, and B is anoligonucleotide of DNA that uniquely identifies X.

MethylC-Sequencing or Bisulphite (BS)-Sequencing

In some embodiments, the internal controls described herein may be usedin BS-sequencing (BS-seq). Bisulfite sequencing is the use of bisulfitetreatment of DNA to determine its pattern of methylation. Treatment ofDNA with bisulfite converts cytosine residues to uracil, but leaves5-methylcytosine residues unaffected. Thus, bisulfite treatmentintroduces specific changes in the DNA sequence that depend on themethylation status of individual cytosine residues, yieldingsingle-nucleotide resolution information about the methylation status ofa segment of DNA. In some embodiments, BS-seq applies routine or“shotgun” sequencing methods on bisulfite-treated genomic DNA todetermine methylation status at CpG dinucleotides. Internal controls foruse with a BS-seq assay include barcoded methylated DNAoligonucleotides, for example, having the configuration X-B, where X isa methylated DNA oligonucleotide, and B is an oligonucleotide of DNAthat uniquely identifies X.

High-Throughput Sequencing of RNA Isolated by CrosslinkingImmunoprecipitation (HITS-CLIP)

In some embodiments, the internal controls described herein may be usedin HITS-CLIP (also known as CLIP-seq) assays. HITS-CLIP is a genome-widemeans of mapping protein—RNA binding sites. HITS-CLIP is similar toChIP-seq, except that proteins bound to RNA (e.g., splicing factors) areimmune-precipitated and the RNA fragments are sequenced. Internalcontrols for use with a HITS-CLIP-seq assay include barcoded RNA-peptideconjugates, for example, having the configuration X-B, where X is anRNA-binding protein, and B is an oligonucleotide of cDNA that uniquelyidentifies X.

Formaldehyde-Assisted Isolation of Regulatory Elements(FAIRE)-Sequencing

In some embodiments, the internal controls described herein may be usedin FAIRE-sequencing. DNA segments that actively regulate transcriptionin vivo are typically characterized by eviction of nucleosomes fromchromatin and are experimentally identified by their hypersensitivity tonucleases. FAIRE refers to a method of isolating nucleosome-depleted DNAfrom chromatin. In some embodiments, the method comprises crosslinkingchromatin with formaldehyde in vivo (in cells), shearing the cells bysonication, extracting the chromatin/DNA by phenol-chloroform extracted.The DNA recovered in the aqueous phase, in some embodiments, issubjected to high-throughput sequencing (FAIRE-seq). Internal controlsfor use with an FAIRE-seq assay include barcoded DNA oligonucleotides,for example, having the configuration X-B, where X is a DNAoligonucleotide, and B is an oligonucleotide of DNA that uniquelyidentifies X.

Micrococcal Nuclease Digestion (MNase)-Sequencing

In some embodiments, the internal controls described herein may be usedin MNase-sequencing. MNase is a method that A method that distinguishesnucleosome positioning based on the ability of nucleosomes to protectassociated DNA from digestion by micrococcal nuclease. In someembodiments, protected fragments may be sequenced to produce genome-widemaps of nucleosome localization. Internal controls for use with anMNase-seq assay include in vitro assembled nucleosomes conjugated tobarcoded DNA oligonucleotides, for example, having the configurationX-B, where X is an assembled nucleosome, and B is an oligonucleotide ofDNA that uniquely identifies X.

Other aspects and embodiments of the invention are further described ininternational application number PCT/US2011/054072, filed Sep. 29, 2011,which claims the benefit under 35 U.S.C. §119(e) of U.S. provisionalapplication Ser. No. 61/387,689, filed Sep. 29, 2010, each of which isincorporated by reference herein in its entirety. The following numberedparagraphs also provide various other aspects and embodimentscontemplated by the invention:

1. A chromatin immunoprecipitation method for parallel processing ofmultiple samples, the method comprising: (a) cross-linking achromatin-associated factor to chromatin; (b) shearing the cross-linkedchromatin of (a) to provide nucleic acid fragments; (c) contacting thechromatin-associated factor cross-linked to the nucleic acid fragmentsof (b) with a first affinity molecule; (d) releasing the nucleic acidfrom the chromatin-associated factor and from the first affinitymolecule; (e) contacting the released nucleic acid fragments in (d) witha second affinity molecule; (f) releasing the nucleic acid fragmentsfrom the second affinity molecule, and (g) optionally isolating thenucleic acid fragments, and (h) optionally analyzing the distributionand enrichment of the isolated nucleic acid fragments, wherein the firstaffinity molecule and/or second affinity molecule optionally is coupledto a substrate suitable for parallel processing of multiple samples.

2. The method of paragraph 1, wherein contacting the nucleic acidfragments in (e) is carried out using an affinity interaction betweenthe nucleic acid fragment and the second affinity molecule.

3. The method of paragraph 2, wherein the nucleic acid is suitablymodified for this interaction.

4. The method of paragraph 3, wherein the modification is addition ofpoly-A tails or biotinylation.

5. The method of any one of paragraphs 1 to 4, wherein the secondaffinity molecule is a poly-T oligonucleotide, avidin or streptavidin.

6. The method of any one of paragraphs 1 to 5, wherein the secondaffinity molecule is silica.

7. The method of any one of paragraphs 1 to 6, wherein the substrate isa surface of a bead or a well.

8. The method of paragraph 7, wherein the bead is a magnetic bead.

9. The method of any one of paragraphs 1 to 8, wherein steps (e) and (f)are not carried out using a purification column or usingphenol/chloroform extraction and ethanol precipitation.

10. The method of paragraph 6, wherein steps (e) and (f) are not carriedout using a purification column comprising silica.

11. The method of any one of paragraphs 1 to 10, wherein the format is a6-well plate, a 12-well plate, a 24-well plate, a 96-well plate, a384-well plate or a 1536-well plate.

12. The method of any one of paragraphs 1 to 11, wherein the firstaffinity molecule in step (c) is an antibody that specifically binds achromatin-associated factor cross-linked to the nucleic acid fragment.

13. The method of paragraph 12, wherein the antibody is coupled to asubstrate.

14. The method of paragraph 13, wherein the substrate is a surface of abead or a well.

15. The method of paragraph 13 or paragraph 14, wherein the substratecomprises protein A or protein G.

16. The method of any one of paragraphs 13 to 15, wherein thechromatin-associated factor binds to the antibody before the antibody iscoupled to the substrate.

17. The method of any one of paragraphs 1 to 16, wherein thechromatin-associated factor comprises an affinity tag.

18. The method of paragraph 17, wherein the affinity tag is FLAG-tag,myc-tag, biotin or DHFR.

19. The method of paragraph 17 or paragraph 18, wherein the affinitymolecule is an antibody that specifically binds the affinity tag, avidinor streptavidin.

20. The method of paragraph 19, wherein the antibody is an anti-FLAGantibody, or an anti-myc antibody.

21. The method of any one of paragraphs 1 to 20, wherein shearing instep (b) is carried out by sonication or micrococcal nuclease digestion.

22. The method of any one of paragraphs 1 to 21, the method furthercomprising a step of analyzing the isolated nucleic acid fragments.

23. The method of paragraph 22, wherein analyzing the isolated nucleicacid fragments comprises determining the nucleotide sequence.

24. The method of paragraph 23, wherein the nucleotide sequence isdetermined using sequencing or hybridization techniques with or withoutamplification.

25. The method of paragraph 24, wherein the techniques are ChIP-Seq,real-time PCR, DNA microarray, or NANOSTRING® array.

26. A chromatin immunoprecipitation kit for parallel processing ofmultiple samples in a multi-well format, the kit comprising:

a) a multi-well plate comprising wells coated on an inside surface ofthe wells with a first affinity molecule that binds to achromatin-associated factor, or is coated with a molecule that binds tothe first affinity molecule, to form a first affinity surface, and

b) a multi-well plate coated with a second affinity molecule that hasbinds nucleic acids, or is coated with a molecule that binds to thesecond affinity molecule, to form a second affinity surface,

optionally further comprising a protein inhibitor, a cross-linkingsolution, a cell lysis buffer, a wash buffer, an elution buffer, and/oruser instructions.

27. The chromatin immunoprecipitation kit of paragraph 26, wherein thekit comprises a single multi-well plate that comprises different wellsfor first and second affinity surfaces.

28. The chromatin immunoprecipitation kit of paragraph 26, wherein thekit comprises a single multi-well plate that comprises wells that haveboth first and second affinity surfaces.

29. A chromatin immunoprecipitation kit for parallel processing ofmultiple samples, the kit comprising:

a) a first bead coated with a first affinity molecule that binds to achromatin-associated factor, or coated with a molecule that binds to thefirst affinity molecule, to form a first affinity surface, and

b) a second bead coated with a second affinity molecule that bindsnucleic acids, or coated with a molecule that binds to the secondaffinity molecule, to form a second affinity surface,

optionally further comprising a multi-well plate, a protein inhibitor, across-linking solution, a cell lysis buffer, a wash buffer, an elutionbuffer, and/or user instructions.

30. The kit of paragraph 26 or paragraph 29, wherein the second affinitymolecule comprises silica.

31. The kit of paragraph 26 or paragraph 29, wherein the second affinitymolecule comprises a poly-T oligonucleotide, a poly-A oligonucleotide,avidin, streptavidin or biotin.

32. The kit of paragraph 26, wherein the multi-well plate is a 6-wellplate, a 12-well plate, a 24-well plate, a 96-well plate, a 384-wellplate or a 1536-well plate.

33. The kit of paragraphs 26 or 29, wherein the molecule that binds tothe first affinity molecule comprises protein A or protein G.

34. The kit of paragraphs 26 or 29, wherein the first affinity moleculecomprises an antibody that specifically binds to a chromatin-associatedfactor, an antibody that specifically binds to an affinity tag, avidin,streptavidin or biotin.

35. The kit of paragraph 34, wherein the affinity tag is FLAG-tag,myc-tag, biotin, or DHFR.

36. The kit of paragraph 34, wherein the wherein the antibody is ananti-FLAG antibody, an anti-myc antibody, or an anti-DHFR antibody.

37. The kit of paragraph 29, wherein the bead is a magnetic bead.

38. A method of preparing an indexed sequence library comprising: (a)purifying or obtaining purified ChIP DNA processed using any one of thepreceding methods; (b) adding unique sequence identifiers to thepurified ChIP DNA; and (c) selecting the ChIP DNA in (b) based on size.

39. The method of paragraph 38, further comprising assessing the ChIPDNA in (c) for enriched molecular binding sites.

40. The method of paragraph 38 or paragraph 39, further comprisingsequencing the ChIP DNA.

41. The method of any one of paragraphs 1-25 or 38-40, wherein themethod is performed using a multi-well format or a microfluidicchamber/channel.

42. The method of any one of paragraphs 1-25 or 38-40, wherein thelibrary is constructed on magnetic particles.

EXAMPLES

The present invention will be more specifically illustrated by thefollowing examples. However, it should be understood that the presentinvention is not limited by these examples in any manner. Other examplesin accordance with certain aspects and embodiments of the invention aredescribed in international application number PCT/US2011/054072, filedSep. 29, 2011, which claims the benefit under 35 U.S.C. §119(e) of U.S.provisional application Ser. No. 61/387,689, filed Sep. 29, 2010, eachof which is incorporated by reference herein in its entirety.

Example 1

A series of different tissues or cells are subjected to genome-widemapping of various histone modifications, one of which is histonetri-methylated H3 lysine 4 (H3K4me3). Pre-determined amounts ofpolypeptide-oligonucleotide conjugates representing either a H3K4me3histone or an un-methylated histone are “spiked” into each tissue/cellsample prior to immuno-precipitation. The samples are then be subjectedto parallel processing and immuno-precipitation. High-throughputsequencing is used to identify the specific genomic sequences enrichedand to determine the degree of enrichment across the tissue/cell samplesanalyzed. The relative ratios of the polypeptide-oligonucleotideconjugates determined in the sequencing step are used to determine theefficiency of H3K4me3 enrichment in each of the parallel assays. Thisinformation is used to normalize the signal data across the multiplesamples (to account for inherent variation in the immuno-precipitationstep), thereby enabling direct comparisons of enrichment values.

Example 2

Four 125 bp DNA strands comprising unique sequences (U) were generated:two complimentary pairs in which the upper strand in each pair wasconjugated to either the peptide recognized by an antibody specific forH3K4me3 (Millipore, catalogue Number: 07-473, rabbit, polyclonal) or thesame peptide without the methylation modification—as a specificitycontrol, that should not be recognized.

IS (1) (SEQ ID NO: 73) ARTK(me3)QTAR (SEQ ID NO: 74)GGC-TGCAGGGACGAGTAGCACATATCGACCAGGAACGAGTAGCACTAGACCCACCGGGAGGAGTAGAAGTAGTTCAGGGTGCGGTAGACCCGGATATGAATGGAGACCCACTACC TCGCGACCGAGGA,(C6-SH modification added to 60th base); (2) (SEQ ID NO: 71) ARTKQTAR(SEQ ID NO: 72)GGC-CTGGCATGCAAGGGGCGGAGGGTGAACGACTAGCACATATCGACCAGGAACGAGTAGCACTAGACCCACCGGGAGGAGTAGAAGTAGTTCAGGGTGCGGTGAAACAGGATGT GAACCGCGATCCT,(C6-SH modification added to 60th base); (3) No peptide- (SEQ ID NO: 76)AGGATCGCGGTTCACATCCTGTTTCACCGCACCCTGAACTACTTCTACTCCTCCCGGTGGGTCTAGTGCTACTCGTTCCTGGTCGATATGTGCTAGTCGTTCACCCTCCGCCCCTT GCATGCCAG;and (4) No peptide- (SEQ ID NO: 75)TCCTCGGTCGCGAGGTAGTGGGTCTCCATTCATATCCGGGTCTACCGCACCCTGAACTACTTCTACTCCTCCCGGTGGGTCTAGTGCTACTCGTTCCTGGTCGATATGTGCTACT CGTCCCTGCA.

In order to evaluate the efficiency of the internal standard (IS), twoChIP experiments were carried out with either the H3K4me3 (Millipore,catalogue Number: 07-473, rabbit, polyclonal) antibody that shouldrecognize IS (1) or with a non-relevant control antibody that shouldrecognize H3K36me3 (Abcam, catalogue Number: ab9050, rabbit,polyclonal), but none of the IS in this experiment. 3×10⁶ mouse ES cellscross-linked with 1% formaldehyde were lysed and then sonicated usingBranson™ sonifier. The samples were then separated into two ChIPexperiments—one for each antibody. The two polypeptide-oligonucleotideconjugates were annealed each with the complementary strand and bothwere spiked to each ChIP. The samples were incubated overnight with thespecific antibodies, and the bound fraction was pulled down(immuno-precipitated) and washed according to published protocols, e.g.(Ku M et al. (2008) Genomewide Analysis of PRC1 and PRC2 OccupancyIdentifies Two Classes of Bivalent Domains. PLoS Genet 4(10): e1000242).DNA was purified using QIAGEN MINIELUTE KIT (QIAgen). The specificimmuno-precipitation was evaluated using qPCR. Using the primersspecific for the H3K4me3-IS: Up primer—TCCTCGGTCGCGAGGTAGT (SEQ ID NO:77); Down primer—GTAGTTCAGGGTGCGGTAGACCCGG (SEQ ID NO: 78), the ratio ofH3K4me3-IS immunopercipitated in the ChIP with H3K4me3 antibody was ashigh as 75-fold over the ChIP performed with the non-relevant antibodyspecific for H3K36me3. Using the primers that amplify the Control-IS: Upprimer—AGGATCGCGGTTCACATCCTGTT (SEQ ID NO: 79); Downprimer—CTGGCATGCAAGGGGCGGA (SEQ ID NO: 80) the ratio between the ChIPperformed with the H3K4me3-specific over the ratio in the ChIP performedwith the control antibody (H3K36me3) was about 1—showing no specificimmunopercipitation. Furthermore, in order to compare betweenenrichments in two reactions of a given peptide, the ratio ofH3K4me3/Control qPCR results from the ChIP performed with H3K4me3 wasdivided by the results of ChIP performed with the controlantibody—H3K36me3. This ratio takes into account the primer efficiency.The resulting enrichment was up to 86-fold of specificimmuno-precipitation of the H3K4me3-IS (Table 1).

TABLE 1 (K4/K36){circumflex over ( )}K4- Pos Cp K4/K36ChIP/(K4/K36){circumflex over ( )}K36-ChIP H3_qPCR K4 A1 20.44 20.41.160704 A2 20.41 K36 A3 20.27 20.6 A4 21.01 H3K4me3_qPCR K4 C1 14.7115.0 30.90996 26.63035951 C2 15.2 K36 C3 19.87 19.9 C4 19.94H3_qPCR_long K4 E1 20.44 20.5 0.861546 E2 20.5 K36 E3 20.6 20.3 E4 19.91H3K4me3_qPCR_long K4 G1 15.19 15.4 37.79177 43.86504976 G2 15.59 K36 G320.37 20.6 G4 20.89 H3_qPCR_short K4 I1 19.51 19.7 0.870551 I2 19.85 K36I3 19.06 19.5 I4 19.9 H3K4me3_qPCR_short K4 K1 14.18 14.5 45.8865752.70982511 K2 14.88 K36 K3 19.85 20.1 K4 20.25 H3K4me3_qPCR_Vshort K4M1 14.03 14.2 75.58353 86.82267696 M2 14.41 K36 M3 20.07 20.5 M4 20.85

Example 3

Internal Standards (IS) Protocol

Each internal standards is provided as a 50 μl aliquot of 20 ng IS. TheIS is diluted accordingly (˜1/5×10⁴), and 10-100 femtograms (fg) of ISare added after the sonication procedure. 100 fg allows enrichment witha H3K4me3 antibody at ˜cycle 26 of qPCR, while 10 fg yields enrichmentat ˜cycle 30.

Primers (mixes of either of the two up primers with each of the fourdown primers, resulting in 8 options). Run qPCR at 65° C. annealingtemperature:

H3K4me3_qPCR_up_long (SEQ ID NO: 81) TCCTCGGTCGCGAGGTAGT H3K4me3_qPCR_up(SEQ ID NO: 82) CGCGAGGTAGTGGGTCTC H3K4me3_qPCR_down_long(SEQ ID NO: 83) TGCAGGGACGAGTAGCA H3K4me3_qPCR_down (SEQ ID NO: 84)ATCGACCAGGAACGAGTAGC H3K4me3_qPCR_down_short (SEQ ID NO: 85)CCACCGGGAGGAGTAGAAG H3K4me3_qPCR_down_60 bp (SEQ ID NO: 33)GTAGTTCAGGGTGCGGTAGACCCGG

EQUIVALENTS AND SCOPE

Those skilled in the art will recognize or be able to ascertain using nomore than routine experimentation many equivalents to the specificembodiments described herein. The scope of the present invention is notintended to be limited to the above Description, but rather is as setforth in the appended claims.

In the claims articles such as “a,” “an,” and “the” may mean one or morethan one unless indicated to the contrary or otherwise evident from thecontext. Claims or descriptions that include “or” between one or moremembers of a group are considered satisfied if one, more than one, orall of the group members are present in, employed in, or otherwiserelevant to a given product or process unless indicated to the contraryor otherwise evident from the context. The invention includesembodiments in which exactly one member of the group is present in,employed in, or otherwise relevant to a given product or process. Theinvention includes embodiments in which more than one, or all of thegroup members are present in, employed in, or otherwise relevant to agiven product or process. Furthermore, it is to be understood that theinvention encompasses all variations, combinations, and permutations inwhich one or more limitations, elements, clauses, descriptive terms,etc., from one or more of the listed claims is introduced into anotherclaim. For example, any claim that is dependent on another claim can bemodified to include one or more limitations found in any other claimthat is dependent on the same base claim. Furthermore, where the claimsrecite a composition, it is to be understood that methods of using thecomposition for any of the purposes disclosed herein are included, andmethods of making the composition according to any of the methods ofmaking disclosed herein or other methods known in the art are included,unless otherwise indicated or unless it would be evident to one ofordinary skill in the art that a contradiction or inconsistency wouldarise.

Where elements are presented as lists, e.g., in Markush group format, itis to be understood that each subgroup of the elements is alsodisclosed, and any element(s) can be removed from the group. It shouldit be understood that, in general, where the invention, or aspects ofthe invention, is/are referred to as comprising particular elements,features, etc., certain embodiments of the invention or aspects of theinvention consist, or consist essentially of, such elements, features,etc. For purposes of simplicity those embodiments have not beenspecifically set forth in haec verba herein. It is also noted that theterm “comprising” is intended to be open and permits the inclusion ofadditional elements or steps.

Where ranges are given, endpoints are included. Furthermore, it is to beunderstood that unless otherwise indicated or otherwise evident from thecontext and understanding of one of ordinary skill in the art, valuesthat are expressed as ranges can assume any specific value or sub-rangewithin the stated ranges in different embodiments of the invention, tothe tenth of the unit of the lower limit of the range, unless thecontext clearly dictates otherwise.

In addition, it is to be understood that any particular embodiment ofthe present invention that falls within the prior art may be explicitlyexcluded from any one or more of the claims. Since such embodiments aredeemed to be known to one of ordinary skill in the art, they may beexcluded even if the exclusion is not set forth explicitly herein. Anyparticular embodiment of the compositions of the invention can beexcluded from any one or more claims, for any reason, whether or notrelated to the existence of prior art.

OTHER EMBODIMENTS

The foregoing has been a description of certain non-limiting preferredembodiments of the invention. Those of ordinary skill in the art willappreciate that various changes and modifications to this descriptionmay be made without departing from the spirit or scope of the presentinvention, as defined in the following claims.

What is claimed is:
 1. A polypeptide-oligonucleotide conjugate of theformula:A-L-N, wherein A is a polypeptide comprising 5 amino acids, L is alinker, and N is an oligonucleotide comprising 10 nucleotides, whereinthe sequence of nucleotides of N uniquely identifies an amino acidsequence and/or amino acid modification of A. 2.-3. (canceled)
 4. Thepolypeptide-oligonucleotide conjugate of claim 1, wherein A comprises anamino acid sequence derived from a histone protein selected from thegroup consisting of histone H1, H2A, H2AX, H2B, H3 and H4. 5.-6.(canceled)
 7. The polypeptide-oligonucleotide conjugate of claim 4,wherein A comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34,35, or 36 amino acids of any one sequence selected from the groupconsisting of SGRGKQGCKARAK (SEQ ID NO: 1), VLLPKKTESHHKAKGK (SEQ ID NO:2), PEPAKSAPAPKKGSKKAVTK (SEQ ID NO: 3), AVSEGTKAVTKYTSSK (SEQ ID NO:4), ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVK (SEQ ID NO: 5),QRLVREIAQDFKTDLRFQSSAVMALQEA (SEQ ID NO: 6),SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLA (SEQ ID NO: 7), and an alteredamino acid sequence of any one or more of SEQ ID NOs:1-7.
 8. Thepolypeptide-oligonucleotide conjugate of claim 1, wherein A comprises anamino acid modification, optionally a post-translational modification.9. (canceled)
 10. The polypeptide-oligonucleotide conjugate of claim 8,wherein the modification is selected from the group consisting ofacetylation, methylation (mono-, di-, tri-), phosphorylation,ubiquitination (mono-, di-, tri-, poly-), sumoylation, ADP-ribosylation,citrullination, biotinylation, and cis-trans isomerization. 11.(canceled)
 12. The polypeptide-oligonucleotide conjugate of claim 7,wherein the alteration is a conservative amino acid exchange, anon-conservative amino acid exchange, or an amino acid exchange of anatural amino acid to a non-natural amino acid. 13.-14. (canceled) 15.The polypeptide-oligonucleotide conjugate of claim 7, wherein thealtered amino acid sequence is 90%, 95%, 98%, or 99% identical to one ofthe amino acid sequences set forth in SEQ ID NOs: 1-7.
 16. (canceled)17. The polypeptide-oligonucleotide conjugate of claim 1, wherein Acomprises:X_(n)Y[M]X_(n), wherein X is an amino acid, n is a number of aminoacids, Y is a modified amino acid, and M is a modification. 18.(canceled)
 19. The polypeptide-oligonucleotide conjugate of claim 17,wherein M is selected from the group consisting of H1 (phospho S1+T3),H1 (phospho S35), H1 (acetyl K63); H2A (asymmetric di methyl R3), H2A(symmetric di methyl R3), H2A (acetyl K5), H2A (mono methyl R17), H2A(symmetric di methyl R77), H2A (Hydroxy P26), H2A (mono methyl K125),H2A (tri methyl K125), H2A (mono methyl K127), H2A (tri methyl K127),H2A (phospho S129); H2B (acetyl K5), H2B (di methyl K5), H2B (HydroxyP10), H2B (di methyl K43); H3 (mono methyl R2), H3 (citrulline 2+8+17),H3 (mono methyl K4), H3 (di methyl K4), H3 (tri methyl K4), H3 (di+trimethyl K4), H3 (acetyl K9), H3 (acetyl K9, phospho S10), H3 (mono methylK9), H3 (di methyl K9), H3 (tri methyl K9), H3 (phospho S10), H3(asymmetric di methyl R17), H3 (acetyl K18), H3 (acetyl K27), H3 (dimethyl K27), H3 (tri methyl K27), H3 (mono methyl K27, tri methylK27+K4), H3 (mono methyl K36), H3 (tri methyl K36), H3 (Hydroxy P38), H3(mono methyl K79), H3 (di methyl K79), H3 (tri methyl K79), H3(mono+di+tri methyl K79), H3 (Hydroxy P121), H3 (tri methyl K122); H4(symmetric di methyl R3), H4 (acetyl K8), H4 (acetyl K12), H4 (monomethyl K20), H4 (tri methyl K20), H4 (phospho T30), H4 (Hydroxy P32), H4(tri methyl K59), H4 (phospho T80), H4 (acetyl K91), and H4 (phosphoT96). 20.-21. (canceled)
 22. The polypeptide-oligonucleotide conjugateof claim 1, wherein N comprises a nucleotide sequence U that uniquelyidentifies an amino acid sequence and/or amino acid modification of A.23.-25. (canceled)
 26. The polypeptide-oligonucleotide conjugate ofclaim 22, wherein N comprises:x_(n)P1-U-P2x_(n), wherein x is any nucleotide, n is a number ofnucleotides, P1 and P2 are primer sequences, and U is a unique sequenceof nucleotides. 27.-31. (canceled)
 32. The polypeptide-oligonucleotideconjugate of claim 22, wherein N comprises:x_(n)Ux_(n), wherein x is any nucleotide, n is a number of nucleotides,and U is a unique sequence of nucleotides. 33.-34. (canceled)
 35. Thepolypeptide-oligonucleotide conjugate of claim 1, wherein A, comprisingeither X_(n) or X_(n)Y[M]X_(n), is joined via a linker L with a N,comprising x_(n)P1-U-P2x_(n).
 36. The polypeptide-oligonucleotideconjugate of claim 35, wherein A-L-N isX_(na)Y[M]X_(na)-L-x_(nn)P1-U-P2x_(nn), wherein X is an amino acid; nais a number of amino acids; Y is a modified amino acid; M is amodification, wherein X_(na)Y[M]X_(na) is least 5 amino acids; L is alinker; x is any nucleotide, nn is a number of nucleotides, P1 and P2are primer sequences, and U is a unique nucleotide sequence. 37.-40.(canceled)
 41. The polypeptide-oligonucleotide conjugate of claim 1,wherein L is a chemical linker.
 42. The polypeptide-oligonucleotideconjugate of claim 41, wherein the linker comprises two reactiveterminal groups that can chemically interact with the two segments A andN.
 43. (canceled)
 44. A set of polypeptide-oligonucleotide conjugatescomprising at least two of the polypeptide-oligonucleotide conjugates ofclaim
 1. 45. (canceled)
 46. A kit comprising thepolypeptide-oligonucleotide conjugate of claim
 1. 47. The kit of claim46, the kit further comprising one or more reagents necessary to performa chromatin immuno-precipitation (ChIP) assay and/or one or morereagents necessary to perform chromatin fragment modification. 48.-51.(canceled)
 52. A method of validating a chromatin immuno-precipitation(ChIP) assay result, the method comprising: (a) obtaining an inputsample of the genomic material of interest and of one or more of thepolypeptide-oligonucleotide conjugates of claim 1, (b) performing a ChIPassay, thereby processing, in parallel to the genomic material ofinterest of (a), the one or more polypeptide-oligonucleotide conjugatesof (a), (c) obtaining a processed sample of thepolypeptide-oligonucleotide conjugate and the genomic material ofinterest processed in (b), and (d) analyzing the samples obtained in(c), thereby obtaining a value and/or signal for each of the analyzedprocessed samples, and (e) validating the ChIP assay result based on thevalue and/or signal obtained in (d).
 53. The method of claim 52, whereinvalidating comprises one or more comparisons of the value and/or signalof the input sample and the value and/or signal of the processed sampleof C1 with the value and/or signal of the input sample and the valueand/or signal of the processed sample of C2, wherein (a) C1 is thegenomic material of interest and C2 is a polypeptide-oligonucleotideconjugate, wherein C2 is a polypeptide-oligonucleotide conjugateimmunoprecipitated with an antibody that is specific for thepolypeptide-oligonucleotide conjugate (C2S), or C2 is apolypeptide-oligonucleotide conjugate immunoprecipitated with anantibody that is non-specific for the polypeptide-oligonucleotideconjugate (C2N), and/or (b) C1 is a polypeptide-oligonucleotideconjugate immunoprecipitated with an antibody that is specific for thepolypeptide-oligonucleotide conjugate and C2 is apolypeptide-oligonucleotide conjugate immunoprecipitated with anantibody that is non-specific for the polypeptide-oligonucleotideconjugate.
 54. The method of claim 53, wherein when (i) the value and/orsignal of the processed sample in (a) of C1 and C2S is significantlyhigher than the value and/or signal of the input sample, then thegenomic sample comprises an epitope specific for the antibody that isspecific for C2S, (ii) the value and/or signal of the processed samplein (a) of C1 and C2N is significantly higher than the value and/orsignal of the input sample, then the genomic sample is non-specificallyamplified and the value or signal obtained is discarded, (iii) the valueand/or signal of the processed sample in (a) of C1 is not significantlyhigher than the value and/or signal of the input sample and the valueand/or signal of the processed sample of C2S is significantly higherthan the value and/or signal of the input sample, then the genomicsample does not comprise an epitope specific for the antibody that isspecific for C2S, (iv) the value and/or signal of the processed samplein (a) of C1 is significantly higher than the value and/or signal of theinput sample and the value and/or signal of the processed sample of C2Sis not significantly higher than the value and/or signal of the inputsample, then the genomic sample is non-specifically amplified and thevalue or signal obtained is discarded, (v) the value and/or signal ofthe processed sample in (b) of C1 is significantly higher than the valueand/or signal of the input sample and the value and/or signal of theprocessed sample of C2 is not significantly higher than the value and/orsignal of the input sample, then the data obtained is analyzed, or (vi)the value and/or signal of the processed sample in (b) of C1 and C2 issignificantly higher than the value and/or signal of the input sample,then the data obtained is not analyzed and is discarded.
 55. (canceled)56. A method of screening an antibody for use in a chromatinimmuno-precipitation (ChIP) assay, the method comprising: (a) contactingan antibody specific for an antigen of interest with one or morepolypeptide-oligonucleotide conjugate of claim 1, wherein at least oneof the polypeptide-oligonucleotide conjugates comprises the antigen ofinterest and at least one polypeptide-oligonucleotide conjugate does notcomprise the antigen of interest (b) performing a ChIP assay, therebyprocessing the oligonucleotide conjugate comprising the antigen ofinterest and the polypeptide-oligonucleotide conjugate not comprisingthe antigen of interest in parallel, (c) obtaining a processed sample ofthe polypeptide-oligonucleotide conjugate in (b), (d) analyzing thesamples obtained in (c), thereby obtaining a value and/or signal foreach the oligonucleotide conjugate comprising the antigen of interestand the polypeptide-oligonucleotide conjugate not comprising the antigenof interest, and (e) comparing the obtained values and/or signals,wherein when the value and/or signal obtained from the oligonucleotideconjugate comprising the antigen of interest is significantly higherthan the value and/or signal obtained from the oligonucleotide conjugatenot comprising the antigen of interest, then the antibody is useful in aChIP assay.
 57. (canceled)
 58. A method of normalizing chromatinimmuno-precipitation (ChIP) assay data, the method comprising: (a)obtaining an input sample of the genomic material of interest and of oneor more of the polypeptide-oligonucleotide conjugates of claim 1, (b)performing a ChIP assay, thereby processing, in parallel to the genomicmaterial of interest in (a), the one or more polypeptide-oligonucleotideconjugates of (a), (c) obtaining a processed sample of thepolypeptide-oligonucleotide conjugate and the genomic material ofinterest processed in (b), (d) analyzing the samples obtained in (c),thereby obtaining a value and/or signal for each of the analyzedprocessed samples, and (e) normalizing the values and/or signalsobtained in (d) for each of the processed samples using the valuesobtained in (d) for each of the input samples.
 59. The method of claim58, wherein parallel processing in (b) comprises contacting the genomicmaterial with the one or more polypeptide-oligonucleotide conjugates.60.-70. (canceled)